Showing posts with label classify. Show all posts
Showing posts with label classify. Show all posts

Tuesday, May 19, 2026

Botanical classification and the theory of evolution [MR #9]

When I made that first post about Tyler Cowen’s monograph on marginalismTyler Cowen has thrown in the towel and is waiting for the machines to take over – I had no specific plays about writing a series of posts about and occasioned by the book. A day later, with a post, Marginalism is a Rank 4 idea, along with thermodynamics and biological evolution, I had decided that, yes, “it looks like I’ll be doing a series of posts about the book, though I can’t say how long that series will be.” But I had no intention of writing as many posts as I have, much less a spin-off working paper, On Method: Computational Compressibility in Complex Natural and Cultural Phenomena.

This post is itself like that. I figured it for two, maybe three thousand words, but possibly less. Instead it’s just grown and grown to over 8000 words (and I dropped a long appendix). There is a reason for that, which you can see in the title of that second post, where I assert that marginalism is a Rank 4 idea. That’s why this series of posts, and this post in particular, has grown. The objective in that second post was to situate marginalism in the context provided by the theory of cognitive evolution that David Hays began publishing in the 1990s starting with our basic paper, The Evolution of Cognition [1]. That’s where we set forth our basic conception that, over the long term, human culture has evolved through a series of architectures each grounded in specific informatic technology, starting with speech (Rank 1), writing (Rank 2), arithmetic calculation (Rank 3), and computation (Rank 4).

On the one hand, since I cannot assume familiarity with those ideas, I have to spend time developing some conceptual apparatus. At the same time I have the opportunity to extent the range of examples Hays and I have subjected to analysis with those ideas. That’s what I’m doing in this post.

In his Chapter 3, Cowen he has remarks about various pinnacles of human achievement, including two moments in the history of biological thinking, the emergence of modern taxonomy in the work of Carolus Linnaeus in the 18th century and the theory of evolution, by Charles Darwin, in the 19th century. I will argue that they represent Rank 3 and Rank 4 cognition, respectively. But I want to start with Rank 1 ethnobiology followed by the Rank 2 ordering of the biological world into a structure that has come to be know as the Great Chain of Being (in the West). This will give us the opportunity to follow one conceptual arena through the four cognitive ranks. Doing that, however, requires developing more conceptual apparatus than I had originally anticipated.

I want to start with how Cowen frames his treatments of botanical classification and evolution and then present some basic conceptual apparatus about processes of perception and cognition. Once those preliminaries have been taken care of we can take a look at the ethnological work on biological classification in Rank 1 (preliterate) cultures. Then we work our way through the other three ranks, commenting on Cowen’s remarks in connection with Ranks 3 and 4, and conclude with some further remarks about Cowen’s peculiar framing.

Cowen’s Framing

There are three aspects to how Cowen frames his various examples, starting, of course with marginalism: lateness, obviousness, and seeing around a corner.

Marginalism is late (p. 57):

To better understand the Marginal Revolution, we need to ask some fundamental questions about economics as a science. In particular, why did it take so long for economic reasoning to develop? I don’t even mean as a full, literal science, replete with advanced econometric methods, but simply as a general conceptual toolbox for intelligent people. The lateness of the Marginal Revolution is part of a broader story about the lateness of economic reasoning more generally.

Later (p. 59):

So I don’t think progress in economics has been slow in general. It is right now coming off an incredible 130-year or so run. Progress in economics, however, was glacial from the time of the ancient Greeks to the late 19th century, with a noticeable burst in the 18th century as well, centered around Adam Smith.

Here he combines all three of factors, peering around corners, obviousness, and then lateness (p. 62-63):

There is no “brute force” method for obtaining fundamental economic insight. Rather, you need to peer around a corner and see something that the other people have not already seen. And once you see and grasp it, you cannot easily forget it, again reflecting the asymmetry of this path toward knowledge. So often I have heard economists make proclamations like: “Once you start thinking about the world in economic terms, you can no longer unsee those things.”

That is exactly correct, but it is truly hard to see them in the first place. In essence, I think economics was so late to develop because it was so hard to peer around its corners. To see supply and demand in their proper workings.

Economics developed late because it is difficult to see around corners where the obvious truths are waiting to be found.

Now we have botanical classification, which Cowen introduces under this heading (p. 65): “Botanical Classification as a Laggard Science.” Then:

The history of botany is a parallel example to that of economics. Some key insights of botany seem fairly intuitive, at least once you understand them, yet they took a long time to develop. [...]

He goes on to remark about how botanical classification should be obvious:

You might think “botany is so simple – all you have to do is to look at a bunch of plants and give them names in some coherent system. They should have mastered this in the Dark Ages!” Surely plants are around us all, and observing them does not require complex equipment such as telescopes.

Cowen frames Darwin’s account of evolution in the same way (p. 76):

Theories of evolution and natural selection also are intuitive once you understand them, and they seem virtually inescapable once you are willing to consider them seriously. Yet they are remarkably late in becoming part of general human knowledge, and indeed to this day, according to polls a significant percentage of Americans still do not accept those doctrines.

Cowen seems to have some idea of the “proper” tempo at which ideas unfold in history but he never offers an explicit account of what this tempo is based on. Rather, he just offers examples of earlier intellectual and cultural high points, e.g. Greek philosophy, geometry and mathematics, Velasquez, Shakespeare, and Bach (pp. 59-61), as if botanical classification could have been cracked in Euclid’s time. Are we to suppose that biological evolution could have been discovered no later than Shakespeare’s lifetime if only someone had peered around the proper corners?

Before moving on to biology, however, I want to lay out some conceptual equipment from cognitive science.

Two Modes of Thought

Decade after decade discussions of thought and perception have settled around an opposition which is expressed in various pairs of terms. I first encountered it as analog vs. digital. In present discussions of AI it presents as neural vs. symbolic. Perhaps the deepest version is the one Miriam Yevick used in 1975, holographic vs. sequential [2]. In a paper David Hays and I published about metaphor we contrasted physiognomic vs. propositional [3].

Most linguistic reasoning exhibits the digital/symbol/sequential/propositional aspect of the opposition. As for the other side of the opposition, the analog/neural/holographic/physiognomic side, I offer this paragraph from the metaphor article that Hays and I wrote:

Our sense of physiognomy, and our use of the term, come from Joseph Church (1966) who talks of the young child, not yet able to read, who can tell one record from another on the basis of the groove patterns on the records. Physiognomic recognition is holistic and analogic. A striking example of this is the “strange friend phenomenon”. You encounter a friend and notice there is something strange about her, but you don't exactly know what. You scrutinize her and finally realize that, e.g. she changed her hair style. Or perhaps you don't figure out what changed and instead must be told. The initial recognition depended on a holistic, a physiognomic representation, not one which explicitly builds a full image from parts and parts of parts. If this initial recognition depended on a scheme which built the whole from the parts then there would be no trouble in discovering what had changed. The part would be found immediately. It is not, it takes time.

A scheme in which the whole is recognized as a composition over an arrangement of parts would be on the other side of the opposition, the propositional side (or digital, symbolic, sequential depending on your intellectual taste).

The reason I say Yevick’s version is the deepest is because she presents it in the context of a mathematical proof. She argues, in effect, that the world contains simple objects and complex ones. Simple objects are most efficiently and accurately recognized by a propositional method (to use the term Hays and I used), while complex objects are most efficiently and accurately recognized holographically. Both are necessary.

I bring the matter up because the distinction is useful in understanding the sequence of biological conceptualizations we’re going to examine.

Rank 1: Ethnobiology and the problem of the unique beginner

Cognitive ethnologists have studied the ways in which preliterate peoples classify life forms [4, 5]. They find that in the regions where preliterate systems overlap modern taxonomy, they are agree on the structural relationships. But there is one anomaly. Preliterate cultures generally lack terms for what they call unique beginners. They’re have terms corresponding to our concepts of fish, snakes, birds, and beasts (i.e. four-legged fur-covered creatures with tails) and our concepts of tree, shrub, grass, and vine, but they lack terms for plant and animal, respectively. But, and this is important, they recognize the distinction between plants and animals by syntactic devices.

What does that mean? All animals can move under their own power; they can sense things (see, hear, smell, touch); they communicate through cries and calls. Plants don’t do any of those things. That means, for example, that animals can be subjects for verbs such as to run, to jump, to look, and to listen, but plants cannot. Similarly, both plants and animals can be subject for verbs such as to grow or to die, but inanimate objects (rocks, houses, bicycles, etc.) cannot. How is it possible to recognize systematic differences in the syntactic affordances of plants and animals without, however, having words to mark those two categories?

As far as I know, there is no accepted explanation for these observations. When I first read them I was incredulous, like Cowen is about the apparent lateness of a variety of ideas. The difference between plants and animals is obvious, no? Well no, not if we accept the ethnographic evidence. As I had no reason to doubt the evidence I was forced to come up with some explanation, if only to satisfy myself.

Here’s what I came up with. The ethnologists have also noted that ethnobiological classifications seem to be based on visual appearance. If we are willing to assume that basic visual classification is based on a physiognomic mechanism, then we can think of it like this:

Creatures having similar appearances are classified together. While fish, for example can be quite different from one another in appearance, any given fish will resemble another fish more than any fish resembles a bird, a snake or a beast. Similarly, any tree will resemble another tree (trunk below, roots in the ground, a large leafy structure above), more than any tree resembles a shrub (shrubs are smaller and the trunk is not nearly so distinct), a grass, or a vine. But what visual comparisons would force arbitrary examples of animals together in one class in distinction to arbitrary examples of plants in a contrasting class? Does it make sense to compare rats with trees, and trout with vines for classification purposes? Do trout and rats resemble one another more than either resembles a pine tree? Those comparisons don’t make sense. They’re distinctly odd.

Monday, June 24, 2019

Should we do away with the categories of Linnaean classification in biology?

Christie Wilcox, What’s in a Name? Taxonomy Problems Vex Biologists, Quanta Magazine, June 24, 2019.
arl Linnaeus was probably not the first scientist to realize the inherent connectedness of life on this planet. But he articulated and codified it. In the 10th edition of his Systema Naturae, published in 1758, he established a system of naming and organizing life that endures to this day — what we still call Linnaean taxonomy, although today’s system is somewhat different from the five-rank hierarchy he proposed. The principle is the same, though: Life is organized into nested ranks, with each higher tier representing a larger group of related organisms to which the species at the bottom belong.

This ranked taxonomy — domain, kingdom, phylum, class, order, family, genus, species — is foundational to biology pedagogy. Every student learns it, often through a mnemonic like “Didn’t Know Popeyes Chicken Offered Free Gizzard Strips” or “Dear King Phillip Came Over For Great Spaghetti.”

But a growing number of researchers think it’s time for taxonomy to move away from these ranks, or even abandon them altogether. “When a student has to learn it, it also suggests to the student that there’s something special about these groups,” said Andreas Hejnol, a comparative developmental biologist at the University of Bergen in Norway. Yet there isn’t.

The problem that Hejnol sees with the whole system is that the ranks don’t mean anything specific or uniform across all groups of life. Even though species is arguably the most important rank across multiple fields of biology, there are dozens of species concepts in use — and biologists working with different groups of organisms can’t seem to agree on just one. You might think that the other end of the hierarchy would be more settled, but it wasn’t so long ago that domains simply didn’t exist — the three domains we use today (Archaea, Bacteria and Eucarya) were only proposed in 1990. At that time, the top rank was kingdom, and there were five of those; now there are at least six, though some say there should be as many as 32. Similar ambiguities plague all the taxonomic ranks in between — even those often considered to be major, distinct and unambiguous, like phyla.
Color me sympathetic, and I haven't even read the article. But I do know something about classification and I've thought about this off and on. Glad to see that some biologists are at least thinking about it. 

Still, given how classification pervades the discipline, it's obvious that changing things, however sensible it seems in the abstract, would be an enormous pain in the posterior. Just how do you get everyone to agree to a new system? How would you propagate such a change and what would happen to the existing literature?

Saturday, August 6, 2011

The Great Chain of Being as Conceptual Structure

This is a bit of mildly technical cognitive science from the archives. It's relevant to a current run of posts about ontology.
Lakoff & Turner (1989) have used a cognitive account of the Great Chain of Being in the analysis of proverbs. I’d like to elaborate on the commonsense structure they call The Nature of Things and suggest an extension.

The Assignment Relation

Consider the table below (adapted from Bloom and Hays, 1978), which moves up the Great Chain. The object in the left-most column is considered to consist of an ASSIGNMENT between the object immediately above it and the object to its right. The general idea is that ontological structure is a pattern of assignment relations.

1) substance
2) thing form
3) living being (plant) vegetative soul
4) animal sensitive soul
5) natural person rational soul
6) social person role

The left-hand column is recognizably the Great Chain and, at this level of argument, rows 1, 2, and perhaps 6 are relatively unproblematic. But what about those souls in lines 3, 4, and 5?

[In the annoying manner of math texts, I leave it as an exercise for the reader to determine whether or not, and if so, just how, juristic persons (corporations) are to be incorporated into this ontology, perhaps as types of social person. I note that this particular issue is under dispute in American politics.]

The first thing to be said is that they are there in Plato and Aristotle and continue in the Western intellectual tradition into the seventeenth century. The second thing to be said is that they are obviously essences, the conceptual purpose of which is to account for the behavior of the beings possessing them. If a plant grows, then, by [the metaphor mapping] EVENTS ARE ACTIONS, it is the vegetative soul that is causing the growing. Things do not have souls and so cannot grow; plants do have them and so can. Similarly, if a dog is sniffing the air and following a scent, it is the sensitive soul which is the source of agency. And so it is for the natural person, speech, and the rational soul.

Tuesday, August 2, 2011

An Ontological Moment in Human Thought?

It's the end of the world!

Are we looking at an ontological moment in human thought?

On the one hand, we have the rise of Object-Oriented Ontology in the Continental philosophical tradition.

But we also have the fact that “ontology” has become a term of art in the knowledge representation division of cognitive science and AI. An ontology, in this sense, is the list of different kinds of things—animal, vegetable, mineral—one must include in a domain model in order to represent that domain in a computer program. As such, it entails no direct commitment to what’s really out there in the world; rather, it’s just how we think about the work.

Q: But how we think about the world is changing, no?

A: Yes.

Back in 1979 psychologist Frank Keil published Semantic and Conceptual Development, which is about how children develop ontological concepts. How do they distinguish living from non-living, and when do they first do it? Plants from animals? Like all good thinkers, of course, he sets it up with a review of the background. There is, way way long ago, Aristotle’s Categories, which he covers, But it’s the more recent history that interests him, Bertrand Russell and Gilbert Ryle, who “proposed theories that relate predictability to ontological categories” and some work originating in logic from the early 1960s by Fred Sommers that encompasses the two.

The notion of ‘category mistake’ is key. For example, “The cow was an hour long” (from Keil p. 3) simply doesn’t make sense. One cannot measure the length of cows in hours (unless, perhaps, one were to ask how long it would take, say, for a small slow-moving animal to move from one end of the cow to another). It’s a mistake in category to make such an assertion.

In this sense, one of the best-known sentences in modern thought is a wonder of category mistakes, Chomsky’s example: Colorless green ideas sleep furiously. Chomsky’s point was that that sentence is perfectly grammatical, but semantically hopeless. Hence, grammar is independent of semantics. He was wrong on that, but that’s another argument.

Saturday, May 22, 2010

Classifying music by rhythmic patterns

I forget where I got this reference, but the article is about the use of automated techniques to classify recorded music into genres according to rhythmic patterns. It is well, if perhaps only informally, known that we can recognize familiar tunes even if we only here the melody's rhythm.

New J. Phys. 12 (2010) 053030
doi:10.1088/1367-2630/12/5/053030


Debora C Correa1, Jose H Saito and Luciano da F Costa

E-mail: deboracorrea@ursa.ifsc.usp.br and luciano.if.sc.usp.br

Published 20 May 2010
Abstract. Online music databases have increased significantly as a consequence of the rapid growth of the Internet and digital audio, requiring the development of faster and more efficient tools for music content analysis. Musical genres are widely used to organize music collections. In this paper, the problem of automatic single and multi-label music genre classification is addressed by exploring rhythm-based features obtained from a respective complex network representation. A Markov model is built in order to analyse the temporal sequence of rhythmic notation events. Feature analysis is performed by using two multivariate statistical approaches: principal components analysis (unsupervised) and linear discriminant analysis (supervised). Similarly, two classifiers are applied in order to identify the category of rhythms: parametric Bayesian classifier under the Gaussian hypothesis (supervised) and agglomerative hierarchical clustering (unsupervised). Qualitative results obtained by using the kappa coefficient and the obtained clusters corroborated the effectiveness of the proposed method.