Species and systematics
evolvingthoughts | December 26, 2008It is often said that one of the most significant discoveries in mathematics was the concept of zero, in the Indus valley sometime in the pre-Christian era. An equally important concept in logic is the operator NOT. While Aristotle, the founder of western logic, had discussed groupings of things in terms of what they are not in the Categories, chapter 10, the importance of NOT seems to have been realised first by George Boole in the nineteenth century. In this post I want to discuss it in the context of classification.
Aristotle wrote of four kinds of "contrarieties":
We must next explain the…
evolvingthoughts | December 23, 2008Damn it's hot. Around here, snow is at a premium, which means our solstitial celebrations are less active than those oop north. Anyway, I got interviewed last night on national radio, the ABC's National Evening show, talking about the early ideas of philosophy to presenter Rhys Muldoon. Nice fellow. It was more like a chat than an interview (which means I did most of the talking, as my chats tend to). It seems I am the sole contactable philosopher in Australia.
So anyway, to entertain you there are some pre-solstitial items just announced. First off, I'm going to put all the internet…
evolvingthoughts | December 14, 2008
Just a couple of days ago I mentioned the Annual Review of Ecology, Evolution, and Systematics. They must have heard me because today I get my email notification that they have published this year's volume. I'd like to mention three papers of interest to me. Alas, children, if you don't have a library subscription (or a personal one), you won't be able to access these papers directly...
To start with the last one first, here's a paper (Coates et al.) that discusses the history and biology of the relationships of early tetrapods - organisms with four limbs, backbones, and bony skeletons. We…
evolvingthoughts | December 12, 2008
There is a widespread tendency of biologists to overgeneralise from their study group of organisms to the whole of biology. Sometimes this is because the organisms are model organisms, like Drosophila (the "fruit flies" that have been used in genetics since the beginning).Other times it is because specialists tend to overestimate the generality of their results and domain. The recent trend to finding "speciation genes" is an example. For some time now various researchers like Chung-i Wu and his collaborators have sought speciation genes. These are genes that cause speciation, in a general…
evolvingthoughts | December 10, 2008I've been travelling a little to organise my move to Sydney. Love the building, the department, the people and the project. Not sure about Sydney... so anyway, nothing of substance from me for a while.
Here's a lovely little essay about Newton pissing off most of the European intellectual giants of his time, by one of our commentators, Thony Christie, at Etherwave Propaganda. He truly was the most egotistical and curmudgeonly bastard of his time, matched only by his actual achievements.
The latest Linnaeus' Legacy is up at Agricultural Biodiversity. They had the good taste to use one of mine…
evolvingthoughts | December 7, 2008Siris has an interesting piece on the nature of the liberal arts. I loves me some 13th century, I does.
Bora objects to Obama's choices being characterised as "elites" and therefore bad. On the other hand, the term "groupthink" was coined to characterise the elite advisors of the first American Camelot. And an open letter to Obama here on the failures of the Healthcare Information Technology proposals in the US. IT won't solve problems that aren't informational in nature.
PM of Notes from the Floating World discusses the constitutionality and sense of the proroguing of the Canadian Parliament…
evolvingthoughts | December 5, 2008
The General Ecosystems Thinking (GET) Group centred at Queensland University of Technology (or as we at UQ like to call it, the "city university") invited me to come give a talk on the ontology of evolution. I gave it yesterday. As it will be part of this series of posts that will end up as some form of publication, I thought you might like to hear my dulcet and husky tones, and read the incredible slide. If so, go here, or get the PDF slides here and the WMA sound here. Check out some of the other speakers too. Thanks to Marco Fahmi for the invite and shepherding.
The actual title was: "…
evolvingthoughts | November 28, 2008
I haven't done much philosophical blogging lately. There are Reasons. I'm preparing to move to Sydney over the next few months (and there may be a period in which I have no laptop too), and trying to catch up on a bunch of projects I have in play and which deserve my attention. Also, there's a stack yay high of books to review. To impress you all and disgust my editors, they include the following:
Books
Sober, Elliott. 2008. Evidence and evolution: the logic behind the science. Cambridge, UK; New York: Cambridge University Press.
This continues Sober's general project of giving a…
evolvingthoughts | November 20, 2008
I'm introducing a new category - the Trashcan. This is a term used in systematics to identify a group that comprises "everything else" once you have done the identification of the real groups of some taxonomic grouping.
I will be using the Trashcan to group together all and only those links that have one common property - that they caught my eye. No other property is necessary or sufficient for inclusion. It has no rank, either.*
Under the fold is the Inaugural Trashcan.
Some work on the simplest vision system, of a marine worm, suggests how complex vision got started. Just two cells…
evolvingthoughts | November 14, 2008
As I have argued before, there is a class of objects in the biological domain that do not derive from the theory of that domain, but which are in fact the special objects of the domain that call for a theoretical explanation. The example I have given is mountain, which is a phenomenal object of geology, and yet not required by the ontology of any geological theory, which does include overfolds, tectonic plates, upthrusts, the process of differential erosion, and so on. At the end of the theoretical explanation, the mountains have not disappeared so that we might now drive from Arizona to Los…
evolvingthoughts | November 12, 2008
So wrote the renaissance humanist, Erasmus of Rotterdam: Man is to man either a god or a wolf. Here, courtesy of Leiter, is an article in The Telegraph, in which philosopher Mark Rowlands describes his life with a wolf, and how he ended up learning, as he puts it, how to be a human from the wolf.
Few animals are as similar in their social behaviour to humans as wolves. The domesticated dog is subordinated to human breeding goals, but the wild wolf is itself - a pack animal with dominance psychology, capable of identifying intentions in other agents, of exploring, teaching and playing. And…
evolvingthoughts | November 11, 2008
There have been several attempts to produce an ontology of biology and the life sciences in general. One of the more outstanding was Joseph Woodger's 1937 The Axiomatic Method in Biology, which was based on Russell's and Whitehead's Principia and the theory of types. In this, Woodger attempted to develop a logic system that would account for all the objects of the theories of biology, especially of embryology, physiology (including cell theory) and genetics. It was hard going even for logicians (Tarski himself wrote an appendix), and the theory thus elucidated seemed to be very post hoc - it…
evolvingthoughts | November 9, 2008
...the albino silverback blinks once or twice, says knowingly "Yes, yes", and sends those who do understand math to these two posts at The n-Category Café: "Entropy, Diversity and Cardinality" post 1, post 2. If I read it aright, it means that diversity is measured as the entropy of some metric space, or the probability distributions of that space. Since this is roughly the same thing as Shannon entropy, it is no surprise to find that ecologists have tricked upon the same equations to deal with this problem. More than that I am not competent to say (curse my teenage lack of interest in…
evolvingthoughts | November 8, 2008
It has become common in recent years for people to use terms of philosophy in distinct contexts, as it has terms of biology. Thus, ontology has gone the way of taxonomy, being dragooned into service of database techniques, to mean something quite the opposite of what it originally meant. I have noticed this tendency of computer technology for decades, ever since I got hopelessly muddled when doing database programming in the early 80s until I realised that they were using some terminology of formal logic in exactly the wrong way (I forget what it was now). A database ontology is not an…
evolvingthoughts | November 5, 2008
I am keen to jot down whatever I can about the ontologies of biology - not just evolution, but also molecular, developmental, taxonomic, ecological and other domains of biology. I want to do this in a relatively systematic manner, so I would appreciate readers noting in the comments the sorts of things/classes/objects that they would like to see discussed, and the domains in which these objects are objects. General categorials rather than specific objects like "humans" or "angiosperms" and the like, please. When we have enough requests I'll sketch out the topics in a later post. Thanks
evolvingthoughts | October 31, 2008
An essay in Nature recently, titled "A question of class" (by Jeffrey Parsons and Yair Wand) puts the case that classification is crucial to science and needs to be understood. They hold, as I do, that a poor understanding of classification - particularly of the concepts/words "class" and "category" - lead to unproductive and dangerous conclusions within science. But I don't think they get there quite yet...
Classification - the act of putting things into classes - is something that every science does, ranging from elements and planets, to diseases, taxa and functions. The authors make the…
evolvingthoughts | October 27, 2008
The NCSE has put up more of its content from it's excellent, if badly laid out, magazine Reports of the NCSE. As a result, one of my better pieces, on species concepts, is now up, with a list of what I at the time thought were the concepts in the modern literature, derived from Mayden's 1997 piece. I would revise the phylogenetic concepts somewhat, but the citations are still useful. Also go check out the revised NCSE website. It has lots of useful links about antievolutionism and evolution. And happy birthday to Genie...
evolvingthoughts | October 26, 2008
The Ediacaran period is the era between around 635Mybp and 540Mybp, just before the Cambrian. You pronounce it "ed-ee-ack-a-ran". It is also the name of a new blog by the inimitable Chris Nedin, erstwhile paleontologist who specialised in the Ediacaran fauna before joining the Dark Side (federal public service) in order to eat. Go read Ediacaran: Past Imperfect and leave some comments. His first post is about why Anomalocaris couldn't continue to eat trilobites. I guarantee that he will be interesting and informed. Bugger knows way too much anyway...
evolvingthoughts | October 22, 2008
That is not a riddle, or rather it's not meant to be, but it's a question worth asking about the barcoding project.
Wired has a nicely written piece about the rationale and program of giving species DNA barcodes and using the gene chosen as the barcode to identify the number of species out there in the world [Hat tip Agricultural Biodiversity]. In it, the founder of barcoding, Paul Hebert, recalls how he came up with the idea:
He says he came up with the idea for the machine in a grocery store. Walking down an aisle of packaged goods in 1998, he indulged in a moment of awe: Here, in a…