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 02, 2005

Ow, my head hurts!

Too much beer. Cooper's Pale, of course. It was the end of the month, and so I had to tie one on. I don't remember much since then. Did I say anything stupid? Why are all these cheques from the Disco arriving in my letterbox?

Seriously, it's good to see even Dembski doing an April Fools riff. As much as I dislike the ideas of the IDevotees, a sensible amount of silly humour is a civilised way to conduct a dispute. I still don't think it's worth serious consideration, intellectually, but at least he isn't trying to lie his way into it, like Wells.

Pity he doesn't respond to detailed criticisms of his views with detailed responses...

Sahotra Sarkar is the proximal source of both our devotion to ID, it seems.

Friday, April 01, 2005

OK, I was wrong. Intelligent Design works

I recently read William Dembski's masterful rebuttal of the "case study" on the evolution of the bacterial flagellum by Nick Matzke, who, it seems, has so many noms de guerre he must be hiding something. I am profoundly ashamed. It seems that ID is not only possible, but necessary. This is my public recantation.

In the past I have accused ID as being epistemic nihilism, a know-nothingness, and a block to future biology. I have called it all kinds of names, such as "non-science", "theology" and "poor philosophy". Well, it seems the joke was on me. Intelligent design is the only thing that can explain how life got to be the way it is. It is simply inconceivable that complex things like flagella could evolve without being caused by the actions and foresight of an intelligent being.

I still don't think this being was God, though. At best, the universe itself is the Designer. An intelligent universe theory is a suitable compromise between the theological arguments from design and a soulless, mechanical universe. Less controversially, there might be purely natural designers, themselves the result of a long process of evolution; much longer than our own - to get the kind of complexity required to be able to "front load" our ancestor's genome with things like the Krebs cycle, flagella, chaperones, and so forth, would require a process of random chance that exceeds anything we could have allowed for purely human evolution. To make it harder still, they would have to be so smart they could prevent inactive genes from drifting into nonsense without selection to maintain them. So I think it is better to assume that the universe is, as Plato thought, a superorganism, with Mind.

This is a red letter day for me. One I will long remember. As I move into the community of scholars who are actively pursuing ID research, expanding the breadth and depth of our knowledge with hard, solid, scientific research programs, I look forward to being able to participate. Those in the Discovery Institute (I apologise for referring to you as "Disco") who wish to involve me in their work should contact me immediately. I can put you in touch with our funding officer to make the arrangements. Say hi to Howard Ahmanson for me.

Yes indeed, I will always remember this day, the first day of April, 2005...

LATE NOTE: I really must give credit where credit is due. Sahotra Sarkar is he who convinced me this was the right course. He should share in the research funds. I apologise for leaving him unmentioned...

Wednesday, March 30, 2005

Species description - creationist

I was bemoaning to Paul Griffiths and Sahotra Sarkar, admittedly over a beer, that unlike them (they are both birdwatchers), I lacked a special organism I could be expert about. This is a grievous fault in a philosopher of biology, so we wondered what I could choose as my "target organisms". Sahotra suggested I name and describe creationists (well, actually he suggested he would, but I'm stealing this from him) as a species. It's important to do this, so that when we describe the behavior of these creatures (pun intended) in the wild, we know exactly what we are discussing. One wouldn't want to claim that a trait found among Old Earth Creationists was true of another geographical or varietal subspecific group. You need to know what you are referring to, as (since I'm name dropping anyway) Maynard Smith said to me when I met him.

So, here it goes. This is done according to proper systematics protocol, so if it's boring, just remember that some systematist somewhere is rolling about laughing.

Species description of creationists

Latin name, author of description and year
Homo troglodytes Linnaeus 1775
Phylum (Division) Chordata
Class Mammalia
Order Primata
Family Hominidae
Genus Homo
Synonyms: None
Common names
  • English: [Christian] Literalists, Bible-believers, Born-again, God-botherer, Evangelical [partial], Creation Scientist, Crevotee, IDevotee, Intelligent Design Creationist
General view of the organism:
Suited with tie, often wearing a cheesy beard (M) or a perm (F) and a broad smile. Can be found selling Amway products. Carries leather-bound King James Version (as produced after 1850) Bible.
Taxonomic description of species
  • Intraspecific forms: subspecies, varieties (Latin names and synonymy), diagnostic characters
Subspecific forms, not geographical:
- Young Earth Creationist
senectus - Old Earth Creationist
propositum - Intelligent Design Creationist
Distribution of species all varieties, within the western world, predominantly North America below the 48 degree N parallel, and above the 30 degree N parallel, between the longitude of 70 degree E and 120 degrees E. Also found in the Middle East, particularly in Turkey.
    General characteristics of species
    • Ecologo-taxonomic group: mostly a benthic bottom-feeder
    • Origin: Los Angeles autochthons, first recorded 1909
    • World distribution: Global but concentrated in English-speaking countries
    • Habitat: Under big tents and in Bible Colleges
    • Migrations: Global migrations, known as "missions"
    Relation to abiotic environmental factors (according to long-term data on distribution and experimental data necessarily with references or through internet links).
    • Relation to salinity: Must be taken with a grain of salt
    • Relation to temperature: prefers hot environments such as law courts, school boards, and legislatures
    • Vertical distribution: Typically stenobathic.
    • Relation to oxygen conditions: Anoxic. Cannot stand fresh air.
    • Feeding type: heterotrophic obligate parasites
    • Feeding behavior: Takes one-tenth of all available resources
    • Food spectrum: agathophagous)
    • Species food supply: undereducated religious believers
    • Quantitative characteristics of feeding: exhibits hyperbolic growth of consumption rate.
    • Reproduction type: logorrhaic
    • Reproduction areas: churches
    • Terms of reproduction: all-seasons
    • Fecundity (or division rate): Unfortunately high
    • Limiting factors: does not reproduce in the presence of science education. Inhibited in the presence of sensible legal barriers.
    Life history and development
    • Life history stages: Juvenile (most do not survive past this stage), adult (declining with age, until an equilibrium frequency is reached at about 40).
    • Age of maturity: Few reach maturity, indeterminate.
    Structural and functional population characteristics
    • Sexual structure: notionally monogamous, prob. polygamous and polygynous (requires future DNA analyses)
    • Population trends: recent increases in English-language regions since 1960; appears to have established a growth cycle of lesser proportions in Muslim nations. Likely to reach plague proportions in some regions of Africa.
    Interspecific relations - symbiotes of Homo evangelisticus, brood parasites on Homo sapiens L.
    Impact on the ecosystem (valid for exotic species) - likely to drive out sensible members of ecosystem if left unchecked.

    Importance of species to bioresources production
    • Economic significance of species: will supplant production based on scientific and technological progress.
    • Commercial characteristics of species, catches: Excellent method of redistributing wealth from the lower middle class to a few fortunate lineages.
    Human impact/threats - under threat from education (see "Reproduction")
    Conservation measures - unnecessary. Likely to overcome ecotypes tolerant of variation
    Forrest, Barbara, and Paul R. Gross. 2004. Creationism's Trojan horse: the wedge of intelligent design. Oxford ; New York: Oxford University Press.

    Numbers, Ronald L. 1992. The creationists. New York: A. A. Knopf : Distributed by Random House.

    Numbers, Ronald L. 1998. Darwinism comes to America. Cambridge, Mass.: Harvard University Press.

    Pennock, Robert T. 1999. Tower of Babel: the evidence against the new creationism. Cambridge, Mass.: MIT Press.

    Pennock, Robert T. 2001. Intelligent design creationism and its critics: philosophical, theological, and scientific perspectives. Cambridge, Mass.: MIT Press.

    Perakh, Mark. 2004. Unintelligent design. Amherst, N.Y.: Prometheus Books.

    Ruse, Michael. 2003. Darwin and design: does evolution have a purpose? Cambridge, MA: Harvard University Press.

    Shanks, Niall. 2004. God, the devil, and Darwin: a critique of intelligent design theory. Oxford ; New York: Oxford University Press.

    Young, Matt, and Taner Edis. 2004. Why intelligent design fails: a scientific critique of the new creationism. New Brunswick, N.J.: Rutgers University Press.

    Compiled by John S. Wilkins
    Acknowledgements Sahotra Sarkar, Talk.origins

    Tuesday, March 29, 2005

    Doing without design

    So, I must continue to deal with design, it seems (curse those lurkers!)...

    I will now move from the boring part - intelligent design and the various other attempts to revivify the argument from design. Let us instead look at design in evolution itself.

    It is commonly said that design, in the guise of adaptation, is a core element of evolutionary theory. I want to make a somewhat radical suggestion - let's lose all mention of it unless we are, as Bacon allowed, talking about human motivations. There is no design in biology. Adaptation is not producing "design-like" or "designoid" objects. There is only ever design in a single place - between the ears of observers of biology, whether they are specialists or naive.

    Design is context-sensitive to the interests of the designer, not the interests of the observer. We project ourselves onto the natural world all the time - we've done this since the earliest recorded times. Plato did it. Aristotle did it less (and the Neo-Platonists Plotinus and Porphyry did it more). But that doesn't mean the world is under any obligation to behave the way we think, or like us. Anthropomorphism is a Bad Thing.

    People, like Dawkins, who say that evolution produces "designoids", or "information", or "function", or "purpose", take ascriptions from the human domain and apply them to the non-human, and non-cognitive domain. We say that a screwdriver has a function because we use it for one. The function of a screwdriver for a manufacturer or retailer is to increase profitability. But the function of an aspect of a living organism is, simply put, whatever the model used to describe and explain it ascribes. When you look at the number of models that can apply to, say, a structural element of a cell like an actin filament or an mRNAse, each one ascribes a function, a purpose or a "design".

    Design and its cognate terms are projections. The question is not whether they are projections, but in what circumstances it increases our knowledge of the things we ascribe them to. In other words, when is the function of a model properly applied to the thing modelled?

    The answer is a purely epistemic one: when the model successfully describes the thing. Actin filaments have a role in the development of, say, William's Syndrome. So the "function" of actin has a role in the normal development of glial cells and neurons. But actin also is a key element in the structural integrity of single celled bacteria. It has a "function" in maintaining and changing shape. It also plays a role in muscle contraction, and cell motility, and so on. Each of these is, in the appropriate (that is, the applicable) context, part of its function. But although it might play a role in sharpening pencils, and in the relevant model it would have that "function", it actually doesn't.

    Designs are abstractions based on how we model things. Functions and goals are likewise. Information is a property of the way a physical structure (usually the primary sequence of a polymer) is symbolically described - you get a different information content when you symbolically describe the primary sequence of a stretch of DNA as "GTAC" than if you described the hydrogen bonds or the numbers of protons or the energy shells of the atoms. It suits us to use the nucleotide abbreviations; but it may also mislead us. Sometimes the weak and strong bonding points on a primary sequence are more important than the sequence itself, biologically speaking, for these will affect folding, expression, and error-correction (this last being an abstract way to speak of mismatch repair).

    So I want to go the whole deflationary hog. Let's stop talking about these abstract properties of biology, and just talk about the biology. What shall we miss? Nothing, since function and goal is only a metaphorical way to express actual physical properties and quantities. Of course, we may continue to use these terms on the understanding that they "stand for" real things, and that the metaphors are only for convenience. Would that it were that simple. We intentional animals keep falling into the trap of mistaking the periphrases for the facts.

    So I want not just a desert ontology, as Quine proposed, but a rigidly physical one, in biology. Evolution is not a process of producing information, goals, or functions. It is a process of physical systems that make more or less accurate copies of themselves in environments of more or less stable thermodynamic and spatial properties. There's nothing that can be called "information" that doesn't involve, in my opinion, a clear analogue to a Shannon system of sender-channel-receiver. Perhaps cell--cell signaling qualifies. Certainly, neural systems do. Genes? Not on your, or any other organism's life.

    Think of the confusion that would be avoided. Think of how we would be able to see clearly that we aren't talking about computers, programs, goals, intentions, purposes or plans. Just living things...

    Bet nobody agrees.

    Monday, March 28, 2005

    Design continued: Rosemary's Garden

    When we design something, we typically make use of prior knowledge and techniques, and of the materials we have used or which hold promise for us on that basis. So, when we explain ordinary design we do this by packing a lot of information into the general model of design processes.

    If I explain why Rosemary has uprooted a garden bed and replanted it with native plants, even though hitherto they had always planted English roses, and had given no indication of why she had done this or that she was about to, my explanation taps into a large body of default and even tacit knowledge of gardening practices, all of which is summed up in the general premise "Gardeners design gardens" or something similar.

    I do not need to have a fully elaborated model of what either Rosemary is likely to do - that is, I don't need a complete or sophisticated model of Rosemary's predispositions to behave - nor do I need to explain why Gardeners occasionally uproot English roses to plant Australian native plants. My explanation is sufficient, so far as it goes, if I note a general tendency of Australian gardeners to plant Australian native plants, so long as it is understood that there are in fact reasons for this (they are more drought-tolerant, require less weeding, and are in fashion because people are coming to appreciate the esthetics of the Australian flora).

    Such a general set of implicit rules makes the outcome "Rosemary replanted her garden with Australian natives" explicable, and indeed, more likely. Moreover, the explanation taps into that tacit knowledge base to assert something about Rosemary - that she is affected by that general set of considerations. To assert that Rosemary's Garden is the product of design is to assert something about her community, culture and the traditions of gardening.

    Now if Rosemary attacked her garden with a hoe, leaving it in a state we would call disarray, we can only know that this is, in fact, disarray in contrast to some kind of Garden-dadaism or Floral Cubism, by making reference to the traditions of design and the expected variations that would count as acceptably Gardening. Maybe Rosemary just had a bad day, or a fight with her Significant Other.

    Explanations fall in what Alan Garfinkel once called a "contrast space" set up by the variables of the question the explanation seeks to address. "Is Rosemary's Garden designed?" specifies a set of alternatives, and these together make a space of possible "yes/no" answers. Garfinkel illustrated this with the famous question asked of bank robber Willy Sutton: a priest asked him why he robbed banks. Sutton answered, "That's where the money is".

    The priest was expecting a moral answer - Sutton robs banks because he needs the money or because he can't get a job. But Sutton has no moral issue here; it's purely a matter of practicalities. He robs banks rather than, say, druggists, because there's more money there. Sutton has a different contrast space than the priest. Explanations are relative to the contrast space required.When I explain that Rosemary's Garden is the product of design, there's a whole set of contrasts I am relying upon.

    But the way the Intelligent Design crowd employ both the notions of "design" (to be a rarified rather than an ordinary notion), and the notion of "explanation", there is no actual contrast space here - all is fluid. All that matters for them is "saving the theology", not "saving the phenomena". So long as something like a God can be made to seem sensible, all is done that need be done. This is not science, and it's not even compatible with science. It is, and remains, epistemological despair, epistemic nihilism, Knownothingness.

    Contrast that with the traditional natural theology that preceded Darwin. It had an honest intent - to uncover the nature of the Deity from the nature of his works. Or contrast it with the reaction to evolution of English Catholicism. The leader of the Oxford Movement, Cardinal John Henry Newman noted that evolutionary biology was not opposed to God or creation, and wrote:

    I have not insisted on the argument from design, because I am writing for the 19th century, by which, as represented by its philosophers, design is not admitted as proved. And to tell the truth, though I should not wish to preach on the subject, for 40 years I have been unable to see the logical force of the argument myself. I believe in design because I believe in God, not in a God because I believe in design.

    [Quoted in Ruse 2003, 72. This is a good, if simplified, introduction to the role design has played in Christian thought in the English speaking world, though I should like to have seem more of John Ray, the founder of natural theology, and of those who followed him in the 18th century.]

    In Germany though, Catholics were less sanguine about evolution due to the aggressive evangelical materialism of Ernst Haeckel. Still, nobody thought that design proved God, or protected theism from science. Newman was happy for science to continue without reference to God. He saw that in science the contrast space of explanations did not include final causes, except, as Francis Bacon noted long ago, with reference to human behavior:

    It is a correct position that "true knowledge is knowledge by causes." And causes again are not improperly distributed into four kinds: the material, the formal, the efficient, and the final. But of these the final cause rather corrupts than advances the sciences, except such as have to do with humanaction.

    [Francis Bacon, Novum Organon, aphorism 3]

    Bacon knew that to assert that design, or teleology, applies to the natural world is a case of what Freud came to call projection - asserting that something natural is like human choice. I will thus finish here with a quotation from the leading critic of design talk in biology, Susan Oyama:
    Powerful and protean and far from being banished from secular science, the argument from design is ubiquitous. Perhaps because we are creatures whose existence and survival depend on our ability to discern regularities in our surroundings and in turn leave our mark, our design, on them, we tend to infer prior design or intent from observed regularity. We formulate, that is, a descriptive rule, which is a form of knowledge, and infer from it a prescriptive rule, which is separate from the processes we see and controls them.
    That's enough about design. It's really rather boring. Next, I will do a series on classification if I can find the time and mental acuity.

    Garfinkel, Alan. 1981. Forms of explanation: rethinking the questions in social theory. New Haven, Conn: Yale University Press.

    Oyama, Susan. 1985. The ontogeny of information: developmental systems and evolution. Cambridge: Cambridge University Press.

    Ruse, Michael. 2003. Darwin and design: does evolution have a purpose? Cambridge, MA: Harvard University Press.