Evolving Thoughts

Evolution, culture, philosophy and chocolate! John Wilkins' continuing struggle to come to terms with impermanence... "Humanus sum, nihil humanum a me alienum puto" - Terence

Saturday, February 25, 2006

Universals and language

I am not a classics scholar, so the following may be completely wrong.

One of the things I have noticed is, no surprise to anybody, that philosophy is full of jargon, like any technical speciality (although we don't hold a candle to biologists). This jargon has grown enormously over the centuries, and it includes such terms as ontology, epistemology, induction, and so on. All of them play specific roles in philosophical discourse (there's another one), and they often stand in for what would otherwise be long definitions and scene setting.

Many of these terms derive from Aristotle, who effectively founded professional philosophy in a range of books (of which we only have a fraction today). And one of the most central is universal. A universal is a term that covers more than one thing, as Aristotle says
Some things are universal, others individual. By the term ‘universal’ I mean that which is of such a nature as to be predicated of many subjects, by ‘individual’ that which is not thus predicated. Thus ‘man’ is a universal, ‘Callias’ an individual. [On Interpretation 17a-17b]
Elsewhere (in Metaphysics 1038b) he says
the substance of an individual is the substance which is peculiar to it and belongs to nothing else; whereas the universal is common; for by universal we mean that which by nature appertains to several things.
Universals became a central problem in philosophy - how can a single concept, word or predicate apply to more than one thing? At the end of the classical period, a commentary on Aristotle's logic by Porphyry of Tyre, known as the Isagoge (Introduction) made the passing comment
As for genera and species, [Porphyry] says, I shall decline for the present to say (1) whether they subsist or are posited in bare [acts of] understanding only, (2) whether, if they subsist, they are corporeal or incorporeal, and (3) whether [they are] separated from sensibles or posited in sensibles and agree with them. For that is a most noble matter, and requires a longer investigation.
"Genus" and "species" here mean something different to the biological sense (that's another story, and a good book could be written about that). It means the general term and the special term that could be defined as a part of the general term.

Whether universals were just in the head or not became a major concern of medieval logicians, leading to the Nominalist position that they were just names, a mere flatus vocus, or breath of the voice. Locke agreed, and started the modern philosophical tradition on that basis.

Even so, it remains a philosophical concern. In 1978, David Armstrong published a significant book defending universals, in a version of Aristotle's account. Some problems never go away.

But I got thinking about Aristotle's account (that a universal is something common to all the substances that fall under the term that defines it). In studying Aristotle's use of the term species, I came to the conclusion that when he used it in biological contexts he meant nothing very technical about it - it was just a common word that meant "kind" or "sort", as Locke said in his Essay. So I wondered if he really did intend to start a technical jargon.

The word Aristotle uses is katholou, from which we get Catholic (the church universal, see?). In the Metaphysics text above he says the katholou is koine (the universal is the common). What does that word mean in Greek, exactly? It is a portmanteau word - formed from kata (according to) and holos (the whole; the insertion of the theta replaces the tau and the aspirant). Etymologically, katholou means "in terms of the whole".

So read this in lay Greek: "the in-terms-of-the-whole is what is common". That's not technical jargon. We might say in English that the term for the whole covers what is shared by all things that fall under it. And put that way, it's pretty much obviously true. We are still left wondering how a term for a whole can apply to all the individual things it does, but it's not quite the metaphysical conundrum it seems if we base our reading on the Latinate tradition fo the middle ages.

Perhaps, and Aristotle scholars can correct me on this, Aristotle is more of a "common sense" philosopher, or even an "ordinary language" philosopher, than we might think. Or perhaps he was just trying to use ordinary language to express ideas exactly. There was a philosopher who died recently named David Lewis (who I was privileged to make a fool of myself in front of once), who used as technical terms basic English words like Big and Large to discuss complex issues of logic. If Aristotle was like Lewis (or Lewis like Aristotle), he can be read much more as a lively thinker than the figure shrouded in twenty five centuries of jargon. I'd love to read that translation. The Barnes edition of Aristotle's works tries, but ends up making him sound more like a logical positivist.

Any Aristotle scholars out there want to try?

Friday, February 24, 2006

Speciation of invaders by natural selection

Continuing my theme of late that species are formed by natural selection even if they are not maintained in sympatry with their nearest relatives that way, comes this item in PNAS by Daniel Funk at Vanderbilt, Patrik Nosil at Simon Fraser, and William Etges from the University of Arkansas.

Funk et al. analysed indices of reproductive isolation (RI) and genetic distance, standing in for the time since speciation, of species that had invaded novel areas and speciated. They used an ecological indicator (ecological divergence, or ED) to see how ecological adaptation and reproductive isolation correlated. They correlated rather well. In over 500 species ranging from flowering plants to birds, fishes, butterflies and other invertebrates, ecological factors correlated strongly with speciation. Somebody who can read statistics needs to comment on this, but it looks to me as if Funk and co. just gave the idea of sympatric speciation a real boost.

The proximate factors here include sexual selection, but even allowing for that, ecological factors on size, diet, habitat selection and so on all indicate that selection plays a crucial role in speciation. Or does it? Nobody denies, not even the most ardent antiadaptationist, that aspects of organisms are strongly subject to selection, whether during speciation or after it. The critical issue is whether selection is a cause of speciation itself.

The allopatric consensus view allows for local adaptation, of course, when isolated from the parent metapopulation. What it denies is that selection for RI occurs - how could it when speciation is occurring without contact with the reproductively isolated populations? There is selection of RI, of course, since RI on that account is a byproduct of changes in the population that are selectively favoured for ecological reasons. But not selection for RI itself [the selection of and selection for distinction is due to Elliot Sober]. So, argue allopatrists such as Jerry Coyne and Allan Orr, selection is not a cause of speciation in allopatry. And this seems right.

The sympatrists claim, on the other hand that some speciation at least occurs when the ranges of the two populations coincide at least in part. In this case, if there is selection for a local adaptive niche that differs from the parental species' niche, there is also selection against hybrids that are equally maladapted for each niche, neither fish nor fowl, as it were. Hence, on a sympatric view, there is selection for RI.

What Funk et al. have demonstrated is that ecology plays a role in shaping the function and structure of new species. This was never really at issue. Does it have any further import?

I think it does. The import lies not in the fact that species are isolated reproductively from their relatives, but that they are cohered with their own by selection. In short, what causes a species is that it is a genetically compatible group with a shared reproductive "reach". And this contributes to the fitness of variants, largely for the very obvious reason that if you can't interbreed with your neighbours, you have a zero fitness. What causes isolation is either geography (allopatry) or divergent selection in sympatry. So being a different species is due to RI; being the same species is due to selection for a range of properties, including reproductive reach and ecological adaptation.

I distinguish between extrinsic and intrinsic selection for this conspecific cohesion. Some aspects of being a species are caused by extrinsic environmental selection - of course we should expect that, for those that cannot flourish cannot breed. But also, in sexual organisms, one has to be compatible with potential mates, and so selection for intrinsic properties that facilitate this must also play a role.

If we think of speciation as "what makes a species" then we get ecological and other selective processes. If we think of speciation as "what makes it not the same species", then the explanatory focus shifts, and here the answer is, in cases when divergent selection is not going on, populations simply drift away from the reproductive reach of the ancestral population.

[Thanks to Pete Dunkelberg for spotting some errors]

Wednesday, February 22, 2006

In America, I'm a Democrat

But in Australia, I don't know what I am. Here's the results from one of those slightly restrictive online tests, this time about political views. [One has to worry about two principal compnent axes in such a complex domain...] Hope this works, you copy their code...

You are a

Social Liberal
(66% permissive)

and an...

Economic Liberal
(25% permissive)

You are best described as a:


Link: The Politics Test on OkCupid Free Online Dating
Also: The OkCupid Dating Persona Test

Monday, February 20, 2006

Aristotle on biology, by Lennox

James Lennox, who is the current expert on Aristotelian biology, has finally delivered his Stanford Encyclopedia of Philosophy article on Aristotle's biology. Why should this matter? Well, Aristotle's influence on biology is both pervasive and constantly misrepresented. He is often triumphally proclaimed to be the master of stupid ideas, like male sperm transmitting the form to the inert maternal substance, in such a way as to show how modern science is the peak of knowledge and freedom from ignorance. And in every case, it's just wrong. Even Darwin thought highly of Aristotle: in a letter to William Ogle thanking him for a copy of his translation of Aristotle's Parts of Animals on 22 February 1882, he wrote, "From quotations which I had seen I had a high notion of Aristotle's merits, but I had not the most remote notion what a wonderful man he was. Linnaeus and Cuvier have been my two gods, though in very different ways, but they were mere school-boys to Aristotle. I never realized before reading your book to what an enormous summation of labor we owe even our common knowledge."

One cannot understand how any aspect of biology developed until one understands Aristotle's contribution and inspiration to it. In my own area, Aristotle is responsible for the development of a logic of investigation (one hesitates to call it "science" as yet) that is the logic of diairesis, or division. The conception of "species" as the smallest group of related individuals comes directly from Aristotle (the term "species" is a Latin translation of the Greek term eidos, from which we also get "idea"). But there were some limitations to the way Aristotle tried to apply this taxonomic notion - it relied on the referents of terms already being natural. Lennox has this to say:

What is clear from the practice of the History of Animals is both the value of division and its limitations. Division by itself does not provide you with the axes of division; rather they are presupposed. Division does not give you animal kinds; as we saw in the previous section, one needs to turn to PA I 4 and HA I 6 for Aristotle's thoughts on how those kinds are established. Something besides division is needed in order for a researcher to recognize theoretically significant kinds. Why group animals together based on their possession of four legs and the ability to produce living offspring (rather than eggs)? Certainly each of these traits is the product of a division, one of modes of locomotion and one of modes of reproduction. But those divisions do not tell you that animals with four legs that bear living young constitute a scientifically significant group.

A second limitation of division is its indifference to the distinction between causally fundamental characteristics and proper attributes, to use the language of the Analytics. Yet, being able to distinguish these is absolutely fundamental to Aristotelian science. A careful comparative study of the History of Animals, on the one hand, and works such as On the Parts or On the Generation of Animals again provides insight into how Aristotle understands and deploys this distinction in his actual scientific practice. And as we have seen above, Aristotle draws explicit attention to its importance for his biological investigations in a number of key texts within those investigations themselves. To study in detail the interplay between definition, causal demonstration and division in the biology is to see Aristotle working through just those problems which form the central question of Posterior Analytics II—how precisely are definition, causal demonstration and division related to one another in the quest for, and achievement of, scientific understanding?

The notion of an "essence" (in Aristotle's terminology, the "what-it-is-to-be-that-thing") is supposed to resolve this. Essential properties were those that a thing needed to have in order to be that kind of thing, but doing science by definition turned out in the longer run to be unsatisfactory (although this didn't become apparent until the 15th century or so), and the empirical turn that followed sat uncomfortably with Aristotle's scientific enterprise.

Modern biology generally tends to avoid using definitions as a way to solve scientific problems, but Aristotelian approaches are endemic. A recent proposal to classify genes according to what is basically the Aristotelian diairesis, the Gene Ontology Project, is gaining ground in part because database structures are basically just diairetic logics. It is useful at explicating much of what we do know but haven't explored yet. But I fear it will constrain investigation in ways we don't expect.

A very long motto for biologists

I believe that the biologist is the most romantic figure on earth at the present day. At first sight he seems to be just a poor little scrubby underpaid man, groping blindly amid the mazes of the ultra-microscopic, engaging in bitter and lifelong quarrels over the nephridia of flatworms, waking perhaps one morning to find that someone whose name he has never heard has demolished by a few crucial experiments the work which he had hoped would render him immortal. There is real tragedy in his life, but he knows that he has a responsibility which he dare not disclaim, and he is urged on, apart from all utilitarian considerations, by something or someone which he feels to be higher than himself. - J.B.S. Haldane, "Daedalus, or Science and the Future," 1923
And what is that? Obviously, grant funding agencies.

[Quote from the comments to this on Pharyngula]

How to get science across to the public

Following up on comments by the maker of Flock of Dodos, PZ Myersh has taken to task the idea that we ought to dumb down our message in order to entertain [summarized by PvM here, with links]. On the Dino List, Kent Stevens posted the following analysis of why science programming is so poor in terms of the sets of audiences and advertisers, which I think needs to be widely available. He has given permission to reproduce it:
The Calculus of Science Documentaries

Regarding the production of science documentaries, it's all about making money, remember. Producers decide on matters of content (e.g., dinosaurs) and delivery vehicle (e.g., Nigel Marvin) as business/marketing issues.


Science documentary producers try to maximize profit (ROI, or Return on Investment) derived from some carefully-targeted set V of viewer. It takes financial investment to create a program. Producers do not merely try to maximize |V| i.e., the size of set V. They also tune their product (the documentary) to target a particular demographic. They seek an audience that is both large AND willing to spend their money on the products of their sponsors. To attract this demographic, what sells?

1) science sells [= attracts science-predisposed viewers, call that set S]. S is a subset of V. That is, some members of V are not really members of S, but landed on a given channel and think Nigel is fun to watch. They are really members of set P (see below). Note that to the extent that science sells, dinosaurs really sell.

2) personality sells [= attracts some other set of viewers, call that set P]. Note that sets P and S are distinct, but not disjoint, i.e. some members of S are also members of P, but |P| >> |S|.

3) sex sells. That's always there in show biz. Just think about "derring do", of wrestling crocodiles, and pith helmets, and safari jackets, and of course, some people find intelligent, witty people attractive. But it might really be just the safari jackets.

Producers understand that as the scientific content (selling point 1, above) is increased, |S| tends to increase but |V| tends to decrease, other factors remaining constant. Too much science puts off some people. In the limit, as the scientific content is maximized, V reduces to roughly S (where |S| = |DML| approximately). So science is introduced, but in moderation.

On the other hand, increasing personality (selling point 2, above) might turn off some diehard members of set S. This is attested by some recent DML postings to this thread.

Producers know what they are doing. As a consultant/talking head in a dozen dinosaur-related documentaries (BBC's WWD, Discovery, NHK, etc.) I have found that most (but not all) producers are open and explicit that their game is to maximize ROI. While the sound guy threads the lapel microphone inside my shirt, I've been reminded to keep it simple, not use big words, and always look excited and dramatic. "Give the viewer no reason to go to the refrigerator" was a recent admonishment.

My advice to the DML is for you individually to maximize the ROI. It's your hour to invest, either in watching the dinosaur show, or American Idol if that's on at the same time, or to contribute to the DML, or to share with your kids, whatever.

Bottom line: dinosaur shows are not meant for you, the members of S. They are meant for ROI.
So, given that we who appreciate and want to teach science are seeking to maximise |S|, the problem is how to ensure that as much as possible this will increase |V|, if we want to maintain a scientifically literate population via the mass media. Personally I think the trick is to ensure that science is taught properly in the first place, requiring a considerable revision of the way it is presented and assessed. That would ensure that |S| was a sizeable subset of |V|. But if we are reduced in the shorter term to using the media to counter the well-funded idiocies of creationist and antiscience organisation, then it pays to consider that ROI.

Free to air television has a number of desiderata, one of which is the cost of filling all that airtime between advertising. Creationists have realised this and offered slick, but of course scientifically useless and vapid, shows for broadcast. It's an expensive business even doing a Ken Burns pan over photos with talking heads style show. So if they get free or mildly licensed stuff with appropriate production values, they'll likely show it.

So we can go some way to meeting the calculus of TV producers while at the same time maintaining our own standards by finding funding to do lots of these shows, each with a bit (just a bit) of good science in it. There's a solution. Go to it...

[Oh, you want money? Ask the Discovery Institute or Answer in Genesis - they have slabs of it.]

The web, evidence and belief

I often find that websites are, well, inaccurate. Shocking to contemplate, but even worse, there is satire out there that is not obvious to anyone who can only read at face value. So to assist in this, I recommend reading Random Perspective. Be sure to read "How to Avoid Being Fooled by a News Satire Story" and "75% of Americans Believe Everything They Read".

Sunday, February 19, 2006

New philosophy of biology blog

Rob Skipper, of the University of Cincinnati, has started a blog worth reading, called hpb etc. The first couple of entries deal with underdetermination in theory development, with the case study being the molecular clock, and parsimony in the Fisher-Wright debate.