Category: Week 3

Jan 19 and 21, due Jan 26

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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?

Continue reading “Week 3 summary + A note on hypotheses and optimisation”
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Week 3

A response to the Lynch reading for Tuesday.

I’ve read the first couple sections, and the section on complexity and nonadaptive processes on page 8600, like Yana suggested. I haven’t read the rest of it.

My first impression was a bit of a “well, of course” situation. It makes perfect sense to me that not all changes are adaptive. It certainly sounds like complexity and directional evolution are contentious within the realm of biologists, which is good to be reminded of.

I found the examples of some species becoming ‘simpler’ really interesting. My first reaction was that of “How do we define ‘simple’ and ‘complex’?” It seemed like the argument in the paper was that of species becoming simpler over time showing that complex isn’t allways better. The examples being salamanders losing their legs and vent-worms going from having two opening to having one. These examples seem to be an assumption along the lines of the ‘if it looks like us it is complex’ complex. What if surviving with no legs or no mouth (in the cases of salamanders and vent-worms respectively) is ‘more complex’ somehow. For example, one might need a bi-directional digestive tract to deal with having just one opening, which takes a very complicated gut to deal with things. I can’t say if this is the case or not, but I am uncomfortable accepting the assumption that X change is a ‘simplification’.

Another question I have is based on the following statement:

“However, the effects of mutation and recombination are nonrandom, and by magnifying the role of chance, genetic drift indirectly imposes directionality ….”

Would someone be able to explain how mutation and recombination are nonrandom? I thought that they were by definition random events that were then selected for/against/neutral.

One last thing I’d like to propose is that maybe a better explanation for the survival/fitness of complex organisms can come from their relatively long life instead of them being better replicatiors? If complex multicellular organisms are not as good at replicating, maybe they just hang around because they take longer to be killed off?

-Scott

A response to the Lynch reading for Tuesday.
I’ve read the first couple sections, and the section on complexity and nonadaptive processes on page 8600, like Yana suggested. I haven’t read the rest of it.
My first impression was a bit of a “well, of course” situation. It makes perfect sense to me that not all changes are adaptive. It certainly sounds like complexity and directional evolution are contentious within the realm of biologists, which is good to be reminded of.
I found the examples of some species becoming ‘simpler’ really interesting. My first reaction was that of “How do we define ‘simple’ and ‘complex’?” It seemed like the argument in the paper was that of species becoming simpler over time showing that complex isn’t allways better. The examples being salamanders losing their legs and vent-worms going from having two opening to having one. These examples seem to be an assumption along the lines of the ‘if it looks like us it is complex’ complex. What if surviving with no legs or no mouth (in the cases of salamanders and vent-worms respectively) is ‘more complex’ somehow. For example, one might need a bi-directional digestive tract to deal with having just one opening, which takes a very complicated gut to deal with things. I can’t say if this is the case or not, but I am uncomfortable accepting the assumption that X change is a ‘simplification’.
Another question I have is based on the following statement:
“However, the effects of mutation and recombination are nonrandom, and by magnifying the role of chance, genetic drift indirectly imposes directionality ….”
Would someone be able to explain how mutation and recombination are nonrandom? I thought that they were by definition random events that were then selected for/against/neutral.
One last thing I’d like to propose is that maybe a better explanation for the survival/fitness of complex organisms can come from their relatively long life instead of them being better replicatiors? If complex multicellular organisms are not as good at replicating, maybe they just hang around because they t

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