Category: Weekly Posts

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Week 7

Non-biological evolution in the literature: Big review by Pagel 2009

Pagel 2009 Nature Rev Genet Human language as a culturally transmitted replicator

Mark Pagel (who is a phylogeneticist) reviews evolutionary modeling of languages, first comparing them to biological evolution (has a nice chart; disagree with a couple points though) and then discussing some recent examples of applications of evolution, including statistics (which should be much more oft used in the humanities, as it is by no means restricted to sciencey things!), phylogeny, analyses of evolutionary rates and evolution of language structures, etc.  The phylogeny section features a nice tree of indoeuropean languages, which looks eerily like Ciccarelli et al 2006 (NB: more updated tree of bacteria here: Wu et al 2009 Nature) In fact, I hijacked that detail for this poster that never got properly released…

The rate of word evolution section discusses an earlier study on lexical replacement being dependent on frequency of word use. Afterwards, Pagel discusses another study comparing language and species diversity and finding a curious correlation between the two (Which makes sense since environments favouring biological diversity may well also favour linguistic and cultural diversification). Then, he discusses the relationship and potential co-evolution of word order and pre- vs. postpositioning of modifiers. He also discusses word order changes and their evolutionary history revealed by phylogenetic analyses of various language families, which reveals interesting patterns like the instability of certain word order states. Pagel then wraps up the review by pointing out that languages, like genomes, have been subject to selective forces throughout their existence, and it would be interesting to investigate why some features, despite being possible, are never or seldom found compared to other features. Overall, this review shows there is ever-growing potential in this field, and hopefully it will develop into a proper science being done with the necessary caution, as opposed to the idle philosophising that plagues some corners of evolutionary linguistics…

(going section by section should help your paper reading+summarising as well…very nice of them to have headings!)

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Week 6

Peter’s Midterm Thoughts

Honestly, I’d kind of like to see a bit more emphasis on absorbing the material; for my part, and I know this is my fault, I do feel like some of it just went in one ear and out the other. I know that short of marked evaluations (that I’m pretty sure everyone would like to avoid), there’s not much way to do this.
On that note, I do actually think the individual presentations have been fantastic, but would like to see more of them and a little more direction to those that happen. The ones we did were a little scattershot in terms of focus. This kind of ties back to the idea of me not really fully retaining the details of information presented in class. If we were required to present a couple times on subjects discussed in class, then it would focus us back onto the topics discussed and probably increase retention. Also, it would enforce the interdisciplinary nature of the course more, since we would have to take it into our own hands.
But the discussions we have are great and the points raised are provocative and interesting. It’s stuff that a linguist or a biologist would not normally be exposed to, which makes them all the more valuable.
Also, just as an aside that we may have talked about, I wonder how an econ major or a Business person would look at this course. I wonder how evolutionary thought would apply to different business models, successful and unsuccessful companies, that sort of thing.

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MURC Week 6

Peter’s MURC Reflections

I think it was a great idea for us to present at MURC. Nerve-wracking? Yes. Supposed to be? Certainly! Only real problem I had was the marking based on visuals, but I think that’s for pretty obvious reasons.

That said, I’m going to stick with what I said in class in that I think more time would have been better for our talks; I realize we couldn’t get a single panel to be registered over two time slots, but maybe we could have registered in two parties? I don’t know, I’m just throwing ideas out there at this point.

Also, I would have liked a little more time in class to go over the presentations; I feel like even one more rehearsal would have improved things, since that would have been another set of comments to work with, particularly to see if there were any lingering issues.

Overall, though, I getting us to present at a conference was fantastic. But again, a little more class time (in all stages of the process) would have been good.

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Week 5

Linguistics Overview

Okay, so I was thinking– we really did gloss over just about everything when we ran through linguistics this week. So here’s a brief glossary of particularly important terms:

Allomorphs: Two phonetically similar and semantically identical morphemes that never appear in the same context.
Allophones: Two sounds that are phonetically similar and never appear in the same context.
Cognate: Two words in related languages that are recognizably similar in both sound and in meaning.
Content words: Words that have specific, definable meanings; basically any word in a sentence that’s not a function word is a content word.
Function words: Words that only exist to serve the grammar of the language; they are often difficult to specifically define and short in length. Examples in English include “and”, “but”, “the”, etc.
Morpheme: The smallest linguistic unit that still has meaning.
Phoneme: A sound that is used by a language to distinguish between words.

That’s everything I can explain for now. Comment if you want more info, want additional terms defined/explained, whatever.

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Week 5

Crossover in biology and computer science

Last week, Rosie was talking about how biologists are uncertain about the benefits provided by sexual recombination. Particularly, she said something about how ‘the numbers’ don’t show any benefit to the organism for sexual recombination. If I recall correctly, sexual recombination is crossover (that’s how I’m going to treat it for this post and someone needs to correct me if I’m wrong).

Then, in my computer science class today, we were talking about Stochastic Local Search algorithms, of which Genetic Algorithms are a subset, and the lecture presented the introduction of crossover as the defining factor of GAs. The impression that I got was that, in computer science, crossover was assumed to be beneficial. And since computer scientists are generally good at calculating the generalized efficiency of algorithms, I assumed that there must be some fairly definite benefit provided by crossover, which contradicts what Rosie said about the mathematic benefits of biological crossover not adding up.

If GAs in computer science benefit from crossover and biological evolution doesn’t, then I see three possible outcomes. 1) The analogy between GAs and biology break down in this case – which is the default assumption. 2) The computer scientists haven’t done strict tests of crossover, and it will turn out to be unhelpful, as in biology. Or 3) GAs and biology both benefit from crossover, meaning that there will be mathematical models of the benefit of crossover from computer science which might be able to inform biology.

I have some discussion on these three possibilities. But I’m going to have to hold off for now.

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Week 4

Language/Orthography Relationship

I’m not sure if this actually makes sense, but it’s a thought that’s been kind of bouncing around in my head. Ashley’s presentation on symbiosis got me thinking about the relationship between language and writing.

First off, most writing systems originated as pictographic at one time or another: that is, they started out as rather rough drawings of whatever it was the symbol was to represent. This means that originally, the symbol had more to do with the idea behind the word than the word itself. Since they were not related to the sound of the word in their correspondent language, the symbols could not reflect affixes or other morphology, and therefore any interpretation would have been based entirely on connecting words and word order. This means that reading pictograms would have originally been much more of an art than the pretty straightforward “sound it out” method that we get away with today.

But the really important bit is that reading the pictograms aloud would have not made any sense because of the lack of morphology and proper formations. At best, it would have sounded stilted and forced.

What this means, in short, is that orthography would have had little to do with the language to which it was linked, simply because it was in no way phonetic. If written and spoken language were originally separate and then became merged, it looks a bit – not a lot, mind, but a bit – like a form of symbiosis.

Over time, the common thread of meaning between symbol and sound becomes overwhelming, and the writing takes on features of the spoken language; in the case of the Phoenician alphabet, a phonetic resemblance was required in order to make the symbols match the syntax. In the case of Chinese, none of the languages have much on the way of morphology, so it was enough to stick to more-or-less pictographic representations.

Eventually, the reverse also happens: people mispronounce words based on their spelling and that becomes a largely attested phenomenon in a particular dialect of the language as a whole.

The last point I wanted to make, going back on the “symbiosis” note, was that having a system of writing dramatically improves the chances a language has of a) remaining unchanged, since there’s a constant record to which debates may be referred, and b) spreading, since a language that has a writing system, being more solidified, will tend to resist change more than a language without one.

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Week 4

computer game that teaches an understanding of evolutionary processes?

So I spent the weekend making a computer game with a bunch of complete strangers. We went from nothing to a finished game in 48 hours, with things like sleep deprivation abounding.

In any case, with computer games on the brain, I am wondering how one might create a fun game that teaches the basic processes of evolution. Not the mechanics and dirty work of getting it running (that’s what engineers are for!), but the concepts it would try to incorporate and the abilities it might try to teach.

Let us assume that we are targeting high-school aged students who haven’t yet taken high-school biology. It is difficult to get them involved in studying (because it’s ‘boring’), but if they are really dedicated to the things they find fun and socially acceptable (like games!). They might already have all the formal biology education they’ll ever get, and know Evolution as ‘one of those theories about how animals, y’know, like, change.’

From the topics that we’ve covered so far, which ones would you consider most important? These can be within the context of biology or any other application of evolutionary theory.

How would you frame this in terms of a game?

(I’ll write my own response to this at some point, but I want to hear what others think first.)

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Week 3

An Alternative to Tree Structures

One thing we brought up in historical linguistics was something of an alternative to tree diagrams. Trees are really nice for representing linear branchings and genetic relatedness, but have a hard time describing what exactly is similar between two languages; as such, some people in linguistics have proposed what’s called the “wave model” of linguistics. Here’s a link to the Wikipedia Article.

For those of you who don’t want to read it, I’ll summarize it here. Basically, you put down the names of the languages on paper and then draw lines around certain subsets of them. Each enclosed area represents a single innovation that sets those languages apart from the rest that you’re studying. The primary advantage to it is that it’s based in featural commonalities, so it’s really easy to see what exactly particular languages share. Disadvantages include the fact that they’re painstakingly difficult to draw and to read, and sometimes the person making them screws up and you get lines bleeding into each other… they can be a real mess.

That said, since they allow you to look at certain changes, if you took things like, say, Early Latin, Classical Latin, Late Latin, a couple dialects of Old French, a couple of Middle French, and a couple of Modern French, those lines are going to tell you what sort of changes happened when and how, simply by mapping the linguistic changes onto the fairly well-known historical record of the area and cultures.

Also, wave models can make it very easy to distinguish which features are “genetically” conditioned (that is, those that the language retained from it’s ancestor language) and those that are “areally” conditioned (those that the language assimilated from other nearby languages). All you really have to do is look at the features shared between most of the languages in its area and those that shared between most everything else in its family.

Of course, life’s rarely that simple, since languages move with the cultures that speak them and so often times it’s no easy task to determine why the language has the areal features it does. But I think the idea’s kind of a cool one.

Also, and this is just a side note, we should have a tag for culture.

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Week 3

Very brief thoughts for this week, as my brain is off on a different planet due to some personal stuff, so I haven’t really been in the mindset for nice crunchy analytical thinking for the last few days. So I thought I’d share a point that came up in a conversation between Yana and me on the bus to Safeway last Thursday to go pick up drinks. We were discussing the relationship between drift and neutral evolution, as the two ideas are conflated. Drift, in population genetics, is specifically related to the frequency of alleles already established in a population, rather than dealing with novel mutations. We tend to think of evolution as being strictly about novel mutations, but different alleles of a gene are essentially established mutations within a population. In this sense, drift is basically a subset of neutral evolution – change without selection pressure.

Also completely unrelated, but I had a moment of nerdy glee when I was looking for resources for my proposal and found that Koerner has a book called ‘Is there a universal grammar of religion?’. Sadly it is currently checked out, but I’ll get my hands on it eventually!

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Week 3

Week 3 summary + A note on hypotheses and optimisation

To summarise Week 3:

Tue – intro to phylogenies with Wayne Maddison; discussed some basics of speciation and evolutionary processes as well, in addition to stressing a non-hierarchical view of diversity and evolution (ie. no ‘ladder’ of progression)

Recommended reference for more phylogeny stuff: TR Gregory 2008 Evol Edu Outreach: ‘Understanding evolutionary trees’

For more info on the proper use of the term ‘basal’, see Krell & Cranston 2004 Sys Entomol: ‘Which side of the tree is more basal? — this is for the biologists among us especially! Many of us are guilty of abusing that term…although I’d think it’s ok as long as the other parties all know how phylogenies actually work, as a bit of a dirty illegal shortcut…

Thu – went over some further MURC info, brainstormed ideas for the short presentations, and then discussed that evol psych paper claiming depression is adaptive. Aside from the issues of the paper pertaining to psychology itself, the evolutionary reasoning was rather sketchy. The take-home message was that an adaptationist just-so story can be fairly easily created for just about anything, and just because we can make one up doesn’t mean it’s a useful explanation.

Hypotheses and fitness landscapes

Competing hypotheses and parsimony

Since this topic was brought up in class, I say useful because it’s rather difficult to experimentally reject a hypothesis about something in the past, and adaptationist stories are hard to support either way. We evaluate their likeliness based on understandings of modern organisms (ie. a good hypothesis should have some biological implications we’d be able to trace); but since we’re using ‘functional biology’ (biochem, mol biol, cell biol, physiol, genetics, etc) to explain many of those features anyway, why not just stay with the neutral explanation unless otherwise necessary?

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