3/15/2007

confusion and prokaryotes

One of my recurrent interests is confusion, especially in science. The way I understand this concept is as follows: a term or concept is confused = that term or concept takes 2 or more entities to be one entity (where 'entity' covers individual objects, properties, relations, etc.). In other words, a confused concept or term conflates distinct things. I think the phenomenon of confusion is important in science because part of what happens in many scientific revolutions is that, from the point of view of the new scientific framework, the old scientific framework is confused -- or vice versa. (Re: 'vice versa': Einstein's principle of equivalence, for example, would be seen as an unjustified conflation from the viewpoint of a classical physicist: gravitation and inertia are two separate things, and running them together as Einstein does is an unjustified conflation.)

I've recently started looking at another potential case of confusion in science, but I'm a bit uncertain about it, and would like to air it to get reactions.

In high-school biology class, we are told that the highest/ most basic division among life on Earth is between 2 kingdoms: prokaryotes and eukaryotes. Eukaryotes are all those organisms whose genetic material is encapsulated within a nucleus; Prokaryotes are organisms whose genetic material is not. In other words, Prokaryote=df not-Eukaryote.

However, in the last 2-3 decades, the highest taxonomic level has slowly switched to a three-group classification: Eukaryotes, Archaebacteria, and (Eu)bacteria. Why? The short answer is: "on the molecular level, [archaebacteria] resemble other procaryotes, the eubacteria, no more (probably less) than they do the eukaryotes" (C. Woese et al., PNAS 1990 p.4577).

The upshot for present purposes is that there are actually two distinct highest taxa whose genetic material is not enclosed within a nucleus, viz. the archaebacteria and the eubacteria. From this point of view, it appears that 'prokaryote' conflates the archaebacteria and the eubacteria. But if we recall the earlier characterization of 'prokaryote' as simply 'not-eukaryote,' then 'prokaryote' does not appear to be a confused term. So the question is: Is 'prokaryote' confused, or not? (And why?) I'm happy to hear just intuitions, as well as intuitions backed up with some sort of argument or evidence.

P.s. -- For some readers, this discussion will immediately call to mind Quine's solution to the 'grue' paradox in his paper "Natural Kinds" (in Ontological Relativity and other essays). There, Quine notes that if the predicate P picks out a natural kind, then not-P usually doesn't. A hackneyed example: 'gold' picks out a natural kind (any matter with atomic number 79), but 'not-gold' does not, because it covers many, many completely disparate things -- there are too many ways to be not gold for 'not-gold' to refer to a natural kind.

This might make us think that many/ most predicates of the form not-P are, in fact, confused, since such predicates most often apply to many different natural kinds. All I can say at this point is: that sounds counterintuitive to me... it doesn't feel to me like 'not-gold' conflates distinct things.

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8 Comments:

At 23/3/07, Blogger Kenny said...

Hmm... this instance of a supposed taxonomic division turning out to be paraphyletic (that's the word, right?) doesn't strike me as an instance of confusion in the sense that you mean it. After all, there's still a natural taxonomic division in this particular case, into the eukaryotes and non-eukaryotes, unlike say the distinction between ocean-dwellers and land-dwellers in which both sides are paraphyletic.

There's a single innovation that all eukaryotes share, and naturally all non-eukaryotes lack it. There's no way to make a bipartite division in the evolutionary tree without having at least one side be paraphyletic, unless you take the very earliest split.

As you say, it doesn't look like taking the complement of a useful class should result in confusion, and we don't want there to be only one non-confused taxonomic division.

 
At 23/3/07, Blogger N. N. said...

It seems that there is a strong inclination to make categorical divisons into pairs. I remember being amused at some of the Athenian Stranger's divisons in the Sophist. You think to yourself, 'Another distinction would really be useful here.' Aristotle's taxonomic divisions are much more reasonable (obviously, since they went virtually unchanged for nearly two thousand years), but with a couple of exceptions, he is also driven to divide by pairs.

 
At 25/3/07, Blogger Alex said...

Well, in the prokaryote/eukaryote case -- why couldn't it be that the distinction is still valid, but that we need a further distinction between different kinds of prokaryotes? Prokaryote would be the genus and Archaebacteria / Eubacteria the species.

What I think is more interesting is when one takes one thing for another (for instance, in set theory, subsethood for inclusion, and vice versa) -- and this type of confusion is slightly different from the type of confusion you point to. It has something to do with understanding the boundaries of a concept (normally the center is all right, but the edges are fuzzy).

One final tidbit -- it seems like, if I disagree with someone, either I'm wrong, or the person I'm disagreeing with is wrong. In the case of changes in scientific models, it seems like the student (i.e. researcher) is pointing out to the teacher (i.e. tradition) that her paradigm is incorrect (and rightly so!).

 
At 25/3/07, Blogger Alex said...

Kenny -- can you explain paraphyletic?

 
At 25/3/07, Blogger GF-A said...

Re: "Paraphyletic" -- there is a simple and accurate description (with pictures) on this Wikipedia page.

Kenny's intuitions are appealing to me, and they may be the right thing to say about this example. But let me try one more time to make the case; perhaps I'll fall on my face.

To start with a ridiculously toy example: Imagine someone with massively wrongheaded chemical beliefs, who thinks that there are exactly two chemical elements (where 'element' is understood in the usual way): gold and something else we'll call "nold". Their concept/ term 'gold' is exactly the same as our concept/ term 'gold.' This person believes that every material body is composed out of these two types of stuff. Water, for example, is completely composed of nold. A traditional wedding band is almost completely gold, with a little bit of nold in the cheaper versions. I think we could legitimately consider 'nold' to be a confused term, in that it conflates hydrogen, helium, carbon, etc.

To make the case a bit more realistic, we might think of the four elements of the ancient Greeks as confusing certain of the elements on our periodic table... though I'm not certain of that example, or committed to it.

The point is obviously that "nold" is like "prokaryote": just as our imagined wrongheaded chemist thinks that all material bodies are made out of these two elements, taxonomists until recently thought that all life on the planet belonged to either the kingdom of prokaryotes or of eukaryotes.

Perhaps there is an important disanalogy between 'nold' and 'prokaryote', or perhaps 'nold' is not a confused term -- but I'm not seeing that either of those are true at the moment.
-Greg

 
At 9/4/07, Anonymous Kris Rhodes said...

In your first post, you said you don't think "Not-gold" conflates distinct things. In your latest comment, however, you say you think "nold" is a confused term. Is it that you think conflation is not what is key to confusion? Or rather, do you think that "nold" conflates while "non-gold" does not?

I have an argument in mind in support of the latter statement ("Nold" conflates while "non-gold" does not (necessarily) do so,) but I'll wait to be sure I'm clear what you're trying to say in the first place.

-Kris

 
At 9/4/07, Blogger GF-A said...

Hi Kris --

Thanks for the comment. Yes, I am trying (not particularly well, it seems) to say that "nold" conflates/ confuses distinct elements, while "non-gold" does not. So I'm very interested/ curious to hear how you are going to vindicate that intuition of mine.

My current thought is that if you asked someone who spoke the "nold" language 'How many types of nold are there?' they would say "One," whereas if you asked someone 'How many types of non-gold are there?', they would say "Lots" (or something similar. That gives us a difference between 'non-gold' and 'nold', but I'm not sure it makes the worries Kenny voiced disappear.

 
At 10/4/07, Anonymous Kris Rhodes said...

gf-a,

"Argument" may have been far too strong a word for me to use. But here's, at least, what I _mean_ by saying "nold" conflates while "non-gold" does not.

I think conflation involves taking two _relevantly distinct_ things to be one thing. (So in a way what I'm saying involves an emendation of the definition of conflation which you've given.) What's "relevantly distinct" mean? Well, I'm not sure a general answer to that question can be given. But the meaning can be illustrated by examples.

Take "nold." It is supposed to be a term for use by chemists. But there are substances which are distinct in a way which is relevant to chemistry, but which are not called "distinct" by an attempt at chemistry which uses the term "nold" in the way you've described. Hence, "nold" conflates.

But take "non-gold." We need a story about how the term is supposed to be used. Say it is used by somone in the pursuit of sorting out a pile of pieces of junk where he happens to know that each piece of junk is either all gold nor not at all gold. All he's trying to do is find the gold. In this case, the distinction between a hobby horse and a disk drive is irrelevant to his pursuit, so it is appropriate for him to give a single term which covers both categories. Hence, "non-gold," when used in this way, for this pursuit, does not conflate.

As I said, "argument" was really the wrong word for me to use. I've just articulated a way of talking about the significance of terminology. I can't say I've said anything as to why one should accept talking about it this way. It seems right to me though...

-Kris

 

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