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, April 15, 2006

Taking down the OS X strawman

Here's a great takedown of deluded and ill-informed Windows boosters on the Boot Camp and Workstation advances. If I have a criticism it is that Jason Snell, the author, gives too little credence for the claim that Macs are better than Windows machines for graphics. Anyone who has wrestled with colour profiles for Windows and Macs knows that the Macs are far superior to Windows machines in terms of accuracy or support for getting colour profiles across monitors and output devices than Windows boxen.

Friday, April 14, 2006

The abstract and the concrete in biology

I suspect that as soon as humans evolved a language capable of assigning nouns to types, they started to make abstractions, and to think that abstractions were real things. Abstraction is a necessary part of knowledge if you want to be able to generalise beyond particulars. But it brings with it dangers, and one of these is what Gould (2002) called the fallacy of abstract reification, and more famously Whitehead (a badly misunderstood thinker, in my opinion) called the fallacy of misplaced concreteness. I will call it the reification fallacy because it's shorter and snappier and because renaming ideas is half of philosophy.

The reification fallacy is endemic in biology. We reify (literally, make into a thing) all kinds of terms. "Organism" is one of them. So is "gene", "organ" and so on. Some of these denote a class of concrete objects: there really is a heart in mammalian organisms, for example, and the fallacy lies in thinking that the typical form is the form. In fact, even such a central and gross subsystem as the aortic arch comes in a variety of quite disparate forms. And each individual will have their own variations. But because it is useful to talk about the aortic arch in teaching and so forth, we reify it.

But there are much more abstract objects than organs or genes (and boy is that a contested concept in biology). I have in mind here terms like "function", "form" and the recent addition (since about 1940) to the abstract pantheon, "information". I believe, rather controversially, that these abstract properties are properties of ourselves rather than the organisms. Well, that's the headline. In fact some of the things that get referred to are real enough. Genes certainly do the things that get called information transmission, and organs certainly do the things that get called functions. But their status as information and functions, and the extracting of those processes over all the other processes that the genes do, or the organs do, depend crucially on the interests and focus of the researchers.

So, why do we abstract things? It has to do with the nature of explanation. The standard notion of explanation in the philosophical literature is known as the deductive-nomological (DN) or Covering Law account, and was formulated by Carl Hempel. According to this, an explanation has the form
Covering Law[s] C
Initial Conditions I
Thing to be explained E
This is the form of a logical argument - C & I E, and so E is explained. The covering laws are general propositions of the kind ∀x (Fx) [All xs are F]. In physics, for example, one might use the law that PV = kT (the Ideal Gas Law, where the pressure P, volume V, and temperature T covary according to a constant k that is specified by the nature of the gas). The explanation would then give values to the variables P, and V and k, and conclude that the temperature T, which is measured in a gas, is explained. But the "law" here holds true only within a limited range of conditions (when the gas is not a liquid at high P or a plasma at high T). That is, it is not exceptionless, and is subsumed under atomic theory.

Now in biology, we want to be able to explain (for example) why a tiger or a zebra has stripes. There is no law about this - it relies on the visual acuity of prey (for tigers) and predators (for zebras) in the appropriate conditions. We set up the conditions I so that the covering generalisations make sense of the outcome. Something like "stripes are selected for when other organisms cannot sense the edges of the animal and this affects fitness", thus confounding both prey for the tiger and predators for zebras (a current hypothesis is that zebras confuse the targeting of individual animals in herds). To do this we need to abstract away from the particular animal to the general type. "Striped animal" is a type - but it depends very much on the focus of the person doing the explaining. Another explanation of stripes is due to Alan Turing, who noted that it can form due to gradients of interacting chemical signals that tell skin cells to express coloration or not. [Apocryphally, Turing was asked if he had explained stripes on a zebra, and he replied "Yes, but the whole animal is harder". Here's a Java applet you can play with.]

So we might now ask if there is a natural class of "striped animal". It is surely true that there is, in one sense, for there are animals and they are striped. But whether that class matches the ways evolution generates them - that is, whether "striped animal" is a clearly delineated natural group that can play a role in scientific explanations - it another matter. It might be that we have arbitrarily constructed that class. For instance, is an animal that uses diffraction to confuse its predators or prey a striped animal? How about if the diffraction gratings are linear and aligned in parallel? How far is the class to extend?

The search of suitable abstractions in biology to play a role in explanation has to be balanced against the particularity of biological objects. But we have to do it, and those classes that fail to be general enough and yet true to the particularity of the organisms, that is, fail to be empirically adequate, tend to be eliminated either through neglect by biologists, or by being deliberately abandoned. Such is the dialectic of science.

But sometimes, these abstract objects persist because they are neither obviously false, nor heuristically useless. And yet, they often cause no end of trouble in the thinking of biology. One of these terms, as I noted, is "gene". Griffiths and Stotz [pdf] have enumerated many kinds of meanings for the term in scientific usage. Some of them are mutually incompatible. Each can be replaced with more descriptive and specific terms, but still people persist in talking about "the" gene. And it has some rather difficult implications, which lead people to say things like "humans are genetically determined in their IQ" and so forth. "Gene" gets reified.

One can multiply examples of this in biology. Is there a solution? Obviously, as a philosopher I think that the sort of work done by philosophers of science plays a role. We can analyse some abstractions the way Griffiths and Stotz have done and situate them in a space of conceptual alternatives to show the confusions. Occasionally we might offer our own formulations. Or we might say that this is a necessary aspect of science, as it refines and forms its ideas, and leave the biologists to sort it out in due time. But since biology has a direct application to social debate and policy, I prefer to think that philosophy can offer a useful method for preventing bad ideas becoming the basis for the application of biology to society.

Explanatory reification is a necessary evil, but it needs to be checked from time to time. It is checked by science, and it can be checked by philosophy, if it takes the science seriously. But there is a broader case of explanatory reification that exceeds the science, and that is the way the terms of science and philosophy are misunderstood by the wider public. Partly this is due to the ways that philosophers misconstrue the generalisations of biology. Mostly it is due to the way that scientists promote their ideas, shorn of nuance and empirical content, to the populace. How often do we read press releases about "the gene" for traits such as homosexuality. Biologists know that this can only be an allele (a gene variant) that is causally implicated in that trait, either by being necessary for it not to develop (that is, its absence causes the trait if everything else is equal) or by being part of a complex of genes and developmental systems. But that's a lot of words to put in a news report or a popular science book.

There are worse examples. One of my favourite pet hates is "information". This is an abstraction that usually just means that there is a mapping between one sort of structure (like a DNA sequence) and another (like the sequence of amino acids in a protein, which gets its functional properties from the way it is folded into complex shapes, assisted by other molecules). But it is so attractive a notion, so strong in its grip on our mind, that we generalise it to include aspects of our human intentionality. We start to talk about the "meaning" of genes, to continue our example. We think we can "decode" genes and make inferences about the environments of the past, or that there is something real about the codical nature of genes, such that they are algorithms (another abstraction) that "solve" problems in the world, or represent environments to the organism.

This is a kind of anthropomorphism - we take some abstractions that are, as it were, in the general culture, the folk psychology and categories of ordinary life, and impose them on things for which those categories did not (culturally) evolve. And scientific images are just those sorts of things. It has been known since the beginnings of science that it contradicts "common sense" notions, of how things behave. And it misleads us systematically. Take "function" - the Aristotelian tradition has this (as "final cause") as something that is fundamental to the nature of (living and artifactual) things. More recent versions of functions accounts for them as the outcome of prior selection in the biological or cultural world - a function is whatever it is that selection has selected for (so-called Proper Functions). So "function" is a post hoc property, not a prior fundamental property.

But I think we can go further and say, that "function" is something that is not only post hoc, but even more post hoc - it is something about the way the organism has evolved, but which also depends upon the things being identified and evaluated by the observer (the scientist). That is, a function is what an observer identifies and explains as being the result of selection for that behaviour or process. But we do not make this kind of caveat, not even implicity, when we ascribe functions. We, to use the terms of critical theory, "privilege" the thing being explained.

A few years back I was talking to a cell biologist working on the role of the actin cytoskeleton in Williams' Syndrome - I believe I've mentioned this before - who bemoaned the fact that in the literature, the "functions" of the actin cytoskeleton (the network of actin filaments that give cells their shapes and structure, among other things) were too many. He wasn't interested in those functions. They interfered with what he was interested in. So there is an explanatory relativity to functions. Whether they were important or not depends on what the cognitive interests of the observer are. But the way philosophers of science (and scientists who do philosophy) talk about them, functions are properties of the world. Rather, we should say, they are properties of the ways the world is modelled or not.

This is basically the old problem of nominalism that arose during the middle ages. Are "universals" (general propositions) in the world or are they in the head? Nominalists, including the very influential Locke, say they are in the head. Am I therefore adopting a radical nominalism here? I think I am, partially, but not entirely. These generalisations occur in our best representations of the world. Like physical laws, they are supposed to identify aspects of the world that are common to all the things being explained. There is a two-way process of accommodation going on here. Our representations start, usually with some folk taxonomy or phenomenological salience, as rough first approximations. Evidence forces us to refine them, while we strive to say as much as can be said about the aspects of the world that interest us. It's not that these general properties don't have any purchase in knowledge of the world, but rather than they are an attempt to shape our representations to express as much as we can about it, as economically as we can, while remaining empirically adequate. One might define science as the process of saying as much as we can as simply as we can based on what we know.

So while the abstractions exist in our heads, and not in the world, they are good representations (or, if you are unscientific, bad ones, though perhaps good representations of social norms) of the world. So where's the fallacy? The fallacy lies not in making inferences from our models and representations, such as making predictions. As I argued above, that is what they are for. The fallacy lies in taking the abstractions at face value; that is, inferring that secondary properties are real because the model works. Or worse, inferring from our cognitive necessities to the reality of the those necessities in the world. There are too many empirically equivalent models, and too many possible cognitive systems, to think that what is true, for contingent historical reasons, of us, must be true of the world we know.

Consider, as a thought experiment, what might have happened had DNA's structure and processes been discovered before "information" was the go in science, say around 1900. We would not be talking about genetic information now, but rather about something like the "factorial power" or "causal efficacy" of genes. Mendel first called his particles "factors" (from the Latin, of course, for "maker"). Information sounds, when you put it like this, like the virtus dormativa of Moliére's play. Or take "function" - what would we talk about if Aristotle's works hadn't been rediscovered in the 14th century? Philosophical problems sometimes arise because of cultural contingencies. The purpose ("function"? "goal"? "telos"?) of science is to eliminate these cultural artifacts in favour of the representations that are as dependent on the world as possible, and on the culture as little as can be realistically achieved.

I think I'll leave it there. A Good Friday sermon, since I'm doing a lot of these lately.

Thursday, April 13, 2006

Windows and Mac 2: A new hope

Well that didn't take long. A company called Parallels has developed (in beta form now) a way of running any version of Windows, Linux, OS/2, Solaris, or DOS, to name a few, as virtual computers on an Intel Mac, which they call Workstation. Moreover, you can run them simultaneously.

So, assuming we put some version of Windows and a Linux, the OSes available on your Mac Intel would be:

1. Unix BSD V
2. OS X
3. OS 9
4. Linux, and
5. Windows

And that's not to mention all the Atari, Commodore 64, etc, emulators out there.

When this technology beds down a bit. the Mac is going to be simply the most flexible computer there is. Even though Parallels also make a Workstation for ordinary Windows boxen, it won't ever run OS X or OS 9.

Now, where did I put that piggy bank?

What Pianka really thinks

Pianka has a short essay entitled "What nobody wants to hear, but everyone needs to know" on his home page. I'm going to quote most of it here and intersperse some commentary:
I have two grandchildren and I want them to inherit a stable Earth. But I fear for them. Humans have overpopulated the Earth and in the process have created an ideal nutritional substrate on which bacteria and viruses (microbes) will grow and prosper. We are behaving like bacteria growing on an agar plate, flourishing until natural limits are reached or until another microbe colonizes and takes over, using them as their resource. In addition to our extremely high population density, we are social and mobile, exactly the conditions that favor growth and spread of pathogenic (disease-causing) microbes. I believe it is only a matter of time until microbes once again assert control over our population, since we are unwilling to control it ourselves. This idea has been espoused by ecologists for at least four decades and is nothing new. People just don't want to hear it.
[Translation: we humans are setting up the conditions for nasty diseases]
Population crashes caused by disease have happened many times in the past. In the 1330s bubonic plague killed one third of the people in Europe's crowded cities. Smallpox and measles decimated Native Americans when Europeans transported them to the new world. HIV is a relatively new disease wreaking havoc in Africa and Asia. Another population crash is inevitable, but the next one will probably be world-wide.
[History shows we have suffered from pandemics in the past, and we can inductively conclude we will again]
People think unrealistically because they have lost touch with the natural world. Many people today do not really know where and how our food is produced, and on what our life support systems are based. As we continue paving over natural habitats, many think that we can disrupt and despoil the environment indefinitely. We have already taken half of this planet's land surface. Per capita shares of all the things that really matter (air, food, soil, and water) are continuously falling. Our economic system is based on the principle of a chain letter: growth, growth, and more growth. Such runaway growth only expands a bubble that cannot be sustained in a finite world. We are running out of virtually everything from oil, food and land to clean air and water.
[We are using more resources than we can sustain]
Some politicians, economists, and corporations want us to believe that technology will come to our rescue. But we have a false sense of security if we think that science can respond quickly enough to minimize threats from emerging diseases. Microbes have such short lifecycles that they can evolve exceedingly fast, much faster than we can respond to them. Many bacteria have evolved resistance to most antibiotics, and viruses are resistant to just about anything. Defense always lags behind offense. So far, modern humans have just been lucky. A reactive approach to problems isn't enough, we also need to be proactive and anticipate problems before they become too severe to keep them from getting out of control.Many people believe that Earth and all its resources exist solely for human benefit and consumption, this is anthropocentrism. We should allow the millions of other denizens of this Earth some space to live -- they evolved here just as we did and have a right to this planet, too.
[Technology will not be able to solve the problem because disease evolves faster than technology can]
I do not bear any ill will toward humanity. However, I am convinced that the world WOULD clearly be much better off without so many of us. Simply stopping the destruction of rainforests would help mediate some current planetary ills, including the release of previously unknown pathogens. The ancient Chinese curse "may you live in interesting times" comes to mind -- we are living in one of the most interesting times humans have ever experienced. For example, consider the manifold effects of global warming. We need to make a transition to a sustainable world. If we don't, nature is going to do it for us in ways of her own choosing. By definition, these ways will not be ours and they won't be much fun. Think about that.
[The ecosystem would be more viable if we didn't do what we do, and if we don't stop it, disease will end up culling the human population]

So, let's consider each of these claims, as I have summarized them:

1. we humans are setting up the conditions for nasty diseases
2. History shows we have suffered from pandemics in the past, and we can inductively conclude we will again

This is clearly true. Disease reservoirs exist among human populations and animal populations around the world. Local populations will have adapted to them, either through immunological or genetic pathways, but once they reach "naive" populations, they will be able to spread rapidly.

Paul Ewald, in his marvellously clear book "Evolution of Infectious Disease", argued that the virulence of a pathogen ("virulence" means something like, exploits the host without concern for the host's viability) is determined by the nature of selection in a population. Not the population of the hosts as such, but of the pathogens themselves. Here's why.

Suppose a disease is passed on at a rate roughly equivalent to the reproductive rate of the host (say, you infect a score or less, or it is passed down mostly through your children). Any mutant form of the pathogen will be less fit than a non-mutation, because those hosts infected by the non-mutant won't die before infecting more hosts, while the virulent one will succeed in infecting fewer hosts even though it controls the host's resources that it has infected.

Now suppose that the disease can spread easily, say, through airborne vectors or water. Now, the race is on. The ones that exploit the host and rush on to the next will be fitter than the ones that just sit there quietly doing their thing. So virulence will increase. The reason why AIDS has decreased in virulence in many countries is because the rate of infection was dramatically lowered by the use of condoms. In countries that ignore or oppose the use of condoms, the virulence is higher because the genetic interests of the host and the pathogen do not coincide.

There is no prescription here. Just a statement of the facts. When a pathogen reaches a "naive" population, the more virulent mutants will spread faster than the less virulent ones, because the rate of infection, due to a lack on inherent resistance, is high. Eventually resistance genes (genes that happen to confer some resistance, like the CCR5 allele which blocks some infection by smallpox, bubonic plague, and, as it happens, HIV) will spread, if they exist, and there will be an equilibrium. The Black Death showed this - it killed around one in three. But typically, if the disease uses the same routes to infection as other related diseases, then it is very much less than this. The Spanish Flu epidemic of World War I killed only 2.5%.

3. We are using more resources than we can sustain

I don't see how anyone can deny this. China alone is using coal and oil at a fantastic rate, and the use of wood in South East Asia and South America to feed the paper industry alone is destroying important, nay, vital, ecosystems. What seems to have happened is that we institutionalized the over-use of resources at a rare moment in history, post-War America. And because we did that then, we have falsely inferred that we can always do this. It doesn't help that the economic interests of industries that were founded or made global at that time control most of the policy making in the nations that really count (America, Europe, the "First World"), forcing developing and underdeveloped (even the terms are loaded!) nations to follow suit or lose any self-determination.

4. Technology will not be able to solve the problem because disease evolves faster than technology can

He means "medical technology", but "food production technology" is also at risk. Diseases strike all organisms, including crops. The Botryitis plague of European grapes, the ergot infection of seed grains that sparked the witch craze, and so on show this, but crop diseases are only part of the problem. Moreover, introduced species in ecosystems that are unable to curb their population growth is also going to affect food production, particularly in overcrowded nations.

Note: no prescriptions here either. And nothing new. All this has been known, and stated, many times.

So, what is wrong with Pianka's claims? The "90%" dieoff claim is one I take issue with. There is no evidence that this will happen based on either prior knowledge or immunology, in my view. What is more likely, though, is that reproductive rates will decline as health and food decreases. In short, we might very well be heading for a society of constantly ill people trying to grow food unsuccessfully, hardly the preconditions for a noble life. But as population declines (and the infrastructure that a large population of non-food-producers permits) so will the basis of technological society. If all the linesmen are out growing wheat and cattle, who's going to support my Internet connection? Or maintain telephones? Of deliver post? and so on. The "post-apocalyptic" society so often envisaged in dystopian science fiction may come gradually rather than suddenly. Less dramatic, equally bad, or worse.

Over some suitably long period, yes, the population will inevitably decline to 10%. But it may not happen through pandemics. They will contribute, but they won't be the major cause, I believe.

So, now to the hard question - the one that all the right wing bloviators have jumped on: is this a good thing? Clearly, no. If we could support our society and population indefinitely, while having a working ecosystem that includes fishing, farming and manufacturing, sure it would be good. But, as a matter of fact, we can't. So faced with a hard choice, what is best? That we take steps to solve it ourselves, or face a more or less rapid decline into medievalism, only this time without the hope of getting out of it, because all the materielle we need to do so has already been used...

That isn't social darwinism. It isn't euthanasia or eugenics. It isn't even conservative or radical politics. It's just damned fact. On this, Pianka is right. Somebody should tell the emperor he's wearing too many clothes.

Tuesday, April 11, 2006

The Seguin Gazette-Enterprise didn't hide the Pianka articles

Mike Dunford at The Questionable Authority has done a bit more digging and it transpires that it was a misunderstanding. Good for him correcting the record. So while I stick by what I said otherwise, they didn't take the articles down out of concern for their inaccuracy.

Happy Face on Mars - more proof of ID

Is this evidence that God the Designer wants us all to be happy?

247-270306-06-Co-Gallecrater-01 L,0