Evolving Thoughts

My new blog

Fri, 07 Aug 2009 18:42:33 +1000

For those who come here from old links, my new blog address is

This blog is no longer active.

Evolving Thoughts moves

Sat, 23 May 2009 14:24:19 +1000

So it is farewell...

I have enjoyed blogging here at Seed, who have been generally very good to me given the constraints of herding cats with string they are working under, but it is time to move on. The neighborhood became a little hostile to old fashioned fogies like me, and that's all we need to say.

Many thanks to the cat herders at Seed, Erin, Arikia, and their predecessors, and to Tim who wrastles the technological b'ars. Thanks also to Adam Bly for the opportunity, and to PZ Mangle, who threw me into the back of a black unmarked van and brought me here.

Now, where can you find me? Here:

ET 3, and the RSS feed is here. Tim assures me everything on this site will remain up indefinitely, which is good for those sites that link to various pages, but I will try to reconstruct it all at the new place too.

So, goodbye and hello.

We will resume transmission as soon as we can

Thu, 21 May 2009 00:57:06 +1000

There's some reorganising of my life and blogging going on. I'll announce all the changes to links and stuff in a fortnight or less. Please excuse the dust and noise of the construction behind the plastic sheets.

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No, it's not an ancestor either (probably)

Tue, 19 May 2009 23:14:13 +1000

In addition to the "missing link" trope that is being dished out about the new primate fossil, is another one, more subtle and insidious: it's the ancestor of all primates. How do they know that? Consider a biologically realistic scenario: at the time there were probably hundreds of species of small bodied mammals with tails and feet like that. One of these species may be the ancestor of all primates, but what are the odds that a specimen from that species is the one that was preserved? Just as all primates now look remarkably similar overall, but one may be the common ancestor of a group in 50 million years or so without being the one that is fossilised, the characters of this species may in fact be shared primitive (in the sense of "came first") traits of its group. So-called plesiomorphic traits, or underived traits, are no indicator that the specimen is a member of an ancestral species, only that it is a member of a group of species, one of which was the ancestor. We don't even know what extant species is the ancestor of Darwin's finches, and we have access to their biogeography, molecular properties, development, behaviour and mating systems. How can we be sure this was "the" concestor (Dawkins' term for common ancestor) of all primates?

We've been bitten by this mistake many times before. Archaeopteryx was supposed to be the ancestor of birds. Neanderthals (now spelled without the "h") were supposed to be "primitive" (i.e., came first) humans. Both are regarded as side branches of the lineage leading to birds and humans, but they show many traits that would have been shared with other species of their group at the time. And we rarely have reason to think we have a sufficient record of all species, as the Hobbit shows (it is regarded as not even a descendent of the H erectus hominids we know were in Asia around the right time).

History loses information. To make claims about history one needs positive evidence, ruling out, or at the least making extremely unlikely, alternative hsitories. Phylogenetics does not rule out all alternative histories, just some subsets. Phylogeny can rule out that a species is an ancestor, but it cannot rule it in. "Ida" may be our greatⁿ parent, but equally it may just be a long lost cousin.

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Alpha Fail

Tue, 19 May 2009 04:27:23 +1000

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Philosophy and evolution

Tue, 19 May 2009 04:10:28 +1000

One of the problems that many people have with evolution is not religious, but philosophical. If evolution is true, they think, then we are at sea - nothing is fixed, nothing is determinate, all coherence is gone, as Donne famously lamented of the death of the two-sphere universe and physics. This is, I believe, a valid worry. But it is not new or due to evolution: Heraclitus worried about it, as did Parmenides, and the solutions given by Plato and Aristotle against the atomists were in effect ways to deny that what really counted was changing. They called change "degeneration" or "corruption". The true reality was the forms (εἶδη) that never changed. It was at first not a widely adopted solution, but with the collapse of the Stoic philosophy in the late Roman period, and the rise of Catholic Christianity, it made a comeback and was the "default" view of the next 1200 years.

What in fact does evolution add to the mix of philosophical unease?

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Creative Commons and textbooks

Mon, 18 May 2009 23:12:39 +1000

Anyone who has had to order textbooks for students knows how expensive they are. Here's something that I hope may end up a trend amongst academics: Creative Commons licensed texts. P.D. Magnus wrote a logic textbook, forall x, which he made available under the CC license; and now David Morris of the University of Lethbridge has used it as the basis on which to write an abstract mathematics textbook, Proofs and Concepts. With luck, this is a new dynamic of the new media, that will benefit education even if it takes away some revenue from academic publishers. For work that is fully created (rather than using existing material) it looks to be a good way to get material out there. If demand-publishing sites become more widely available, you can even get a hard copy version done nicely.

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Punnett on Mendelism and species

Mon, 18 May 2009 22:49:21 +1000

The wonderful Project Gutenberg has just released a fully HTMLised version of R. C. Punnett's (he of the famous "square") 1911 book Mendelism, which shows how quickly the implications of Mendelian genetics, rediscovered 11 years earlier, were worked through. It's a wonderful read, and anyone with a slight knowledge of biology and the interest to work through the examples can understand it, something one cannot say of texts on science for very much longer after this. I was particularly interested in the following passage, from page 150:

One last question with regard to evolution. How far does Mendelism help us in connection with the problem of the origin of species? Among the plants and animals with which we have dealt we have been able to show that distinct differences, often considerable, in colour, size, and structure, may be interpreted in terms of Mendelian factors. It is not unlikely that most of the various characters which the systematist uses to mark off one species from another, the so-called specific characters, are of this nature. They serve as convenient labels, but are not essential to the conception of species. A systematist who defined the wild sweet pea could hardly fail to include in his definition such characters as the procumbent habit, the tendrils, the form of the pollen, the shape of the flower, and its purple colour. Yet all these and other characters have been proved to depend upon the presence of definite factors which can be removed by appropriate crossing. By this means we can produce a small plant a few inches in height with an erect habit of growth, without tendrils, with round instead of oblong pollen, and with colourless deformed flowers quite different {151} in appearance from those of the wild form. Such a plant would breed perfectly true, and a botanist to whom it was presented, if ignorant of its origin, might easily relegate it to a different genus. Nevertheless, though so widely divergent in structure, such a plant must yet be regarded as belonging to the species Lathyrus odoratus. For it still remains fertile with the many different varieties of sweet pea. It is not visible attributes that constitute the essential difference between one species and another. The essential difference, whatever it may be, is that underlying the phenomenon of sterility. The visible attributes are those made use of by the systematist in cataloguing the different forms of animal and plant life, for he has no other choice. But it must not be forgotten that they are often misleading. [Emphasis added by me]

It's my opinion that the species problem arose around this time when people started to ask the sorts of questions Punnett raises here: what makes the species genetically? It's also worth noting that he distinguishes between the diagnostic genetic factors that are used to identify species, and those that are causally constitutive, as it were. And finally it's worth noting that this is a fully fledged "biological" species concept, 29 years before Mayr published his.

Hattip to Christopher Elliot at Foundations of Science, Sydney

Quote

Sun, 17 May 2009 20:37:14 +1000

The custom of making abstract dogmatic assertions is not, certainly, derived from the teaching of Jesus, but has been a widespread weakness among religious teachers in subsequent centuries. I do not think that the word for the Christian virtue of faith should be prostituted to mean the credulous acceptance of all such piously intended assertions. Much self-deception in the young believer is needed to convince himself that he knows that of which in reality he knows himself to be ignorant. That surely is hypocrisy, against which we have been most conspicuously warned. [Ronald Aylmer Fisher, BBC broadcast on "Science and Christianity" 1955, from Biographical Memoirs of Fellows of the Royal Society of London, 9: 91-120, (1963), p96]

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Moral atheists

Sat, 16 May 2009 22:35:54 +1000

I find it highly ironic that the people taking the moral stand here are the atheists:

It does not matter if it prevented some sort of attack. It is still a crime, it is still wrong, and those responsible for it deserve criminal prosecution. No amount of talk about 9/11 can change this.

"It", is torture. Yes, it is a war crime, and the people who both did it and authorised it are war criminals. End of story.

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Welcome u n d e r v e r s e

Sat, 16 May 2009 22:17:48 +1000

This is to note that u n d e r v e r s e, the blog that uses nineteenth century German emphatic spacing, has been added to my blogroll (I hope - I'm not good that these customisation things), wherein you can read deep, intelligent and Chamberlainist musings by Chris Schoen. Highly recommended.

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Benson Mates dies

Sat, 16 May 2009 18:41:50 +1000

Leiter reports that Benson Mates has died, and links to the UC Berkeley short obit:

The Department announces with great sadness the death, on May 13, 2009, of Prof. Emeritus Benson Mates. Born in 1919, Prof. Mates studied at the University of Oregon, completing the B.A. degree there in 1940 (in Philosophy and Mathematics). He began work at the graduate level in Philosophy at Cornell, but his studies were interrupted by a stint during the war in the US Navy. He entered the graduate program in philosophy at UC Berkeley in 1945, completing his Ph.D. degree in 1948 after working with (among others) Harold Cherniss and Alfred Tarski. His dissertation was a study of “The Logic of the Old Stoa”. Prof. Mates took up a position in the Philosophy Department at Berkeley in 1948, working as Assistant and then Associate Professor here from 1948–1958; he was promoted to full Professor in 1958, and held that title until his retirement in 1989.

Prof. Mates’s interests ranged widely over problems in logic, epistemology, and the history of philosophy. His influential books include Stoic Logic (1953); Elementary Logic (1965); and The Philosophy of Leibniz (1986). His own philosophical tendencies were sympathetic to strands in ancient skepticism, a theme that emerges clearly in his book Skeptical Essays (1981).

I am very familiar with the linked book - as an undergraduate we worked through it carefully, proving to ourselves the theorems given. I still have my copy, and look at it forlornly in remembrance of when I actually, for a very brief time, understood formal logic. It is a work of art.

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Teeth and a marsupial lion

Sat, 16 May 2009 07:26:07 +1000

Chris Nedin has another post of great interest (even if it is for a late period, the Pleistocene) which goes into my file of "the older naturalists were great observers", as he shows how modern chemistry supports Richard Owens' diagnosis of Thylacoleo as a carnivore, even though it is in a clade of herbivores.

Evolving Thoughts

My new blog

Evolving Thoughts moves

We will resume transmission as soon as we can

No, it's not an ancestor either (probably)

Alpha Fail

Philosophy and evolution

Creative Commons and textbooks

Punnett on Mendelism and species

Quote

Moral atheists

Welcome u n d e r v e r s e

Benson Mates dies

Teeth and a marsupial lion

Actually, it's the process of answering that matters, not the answer

If you don't believe what I believe, you aren't fully human