Month: January 2010

Categories
Uncategorized

Population Genetics Plaything

Okay, so here’s the place you can download the really simple population genetics simulation thingy I mentioned today: http://wps.prenhall.com/esm_freeman_evol_3/12/3315/848837.cw/index.html

Your different alleles (so types of a gene, remember) are labbeld A1 and A2. You can give their respective genotypes fitness values, the higher the fitness #, the more they benefit the organism carrying them. Everything else is pretty self-explanatory, except maybe the inbreeding coefficient, which is the probability f of an individual breeding with a relative (who, by definition, is carrying the same alleles).

Anyways, to see what they’re talking about in the Lynch paper, play around with the population size and fitness levels. I have a screenshot of what I did, but cannot for some reason get it to upload on photobucket…

Categories
Uncategorized

Brief response to Lynch

I can’t say that I enjoyed reading this article very much; all this jargon is beginning to irk me. And then I find my mind wandering off somewhere with more sunlight and trees. Modulation? What?

My understanding is this: evolutionary biology tends to invite broad speculation on the part of non-specialists who think they’re qualified to make assertions based on their high school biology classes. (Which is why I usually only discuss this stuff when I’m drunk–no one’s going to be bothered by my baseless, uninformed opinions.) Why? Because it’s easier and more fun to fit scientific theories into one’s pre-existing ideas than basing these assertions on, say, observable data. The latter tends to take more work, an open mind, and all sorts of nonsense like that. Since evolutionary biology encompasses many philosophically sensitive topics (mostly just our creation and the reasons why we are the way we are), and since billions of years of its history are unobservable due to our irritating lack of time-travelling technologies, all sorts of people (including myself) like to butt in and dole out our two cents. In fact, the longer I take this course, the more evident my indecent lack of knowledge becomes.

But this isn’t as blame-worthy as I’ve ended up making it sound. World views are powerful forces, and not likely to change quickly, excepting some extreme happenstance. So, as we saw with that depression article, scientists of every flavor are not immune to such biases. Essentially, it’s good to remember that deeming a trait as better/worse, adaptive/maladaptive is not very useful and only marginally scientific. I like what someone wrote earlier about complexity: how do we define that, anyway? Because we tend to think that we are the most complex organism out there, just because we have invented things like the can opener and disco. Isn’t simplicity usually more stable, anyway?

Categories
language 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.

Categories
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!

Categories
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”
Categories
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
Categories
Weekly Posts

Here’s my random thought for the week:

So, since I wasn’t able to explain it really well on Thursday, here’s my musing on how it might actually be good for your genes to kill yourself. So as Yana (I think?) was saying, if you’re past the point where you can reproduce, and you’re taking resources away from your children and not contributing much back, the best option is to go off yourself to increase your children’s, little bundles of genes that they are, chance of survival. Now, say that you’re young and fit and in your 20’s, but you’re also a total loser. People of the opposite gender hate you, you’re not particularly good at hunting and gathering and thus mostly rely on other people to get you fed, and your chances of being able to raise a family are pretty slim. Now suppose you have a brother. Your brother is slick and hot and awesome. He already has 15 kids running around, which carry roughly a quarter of your genes. You on the other hand will probably never have kids, and are a drain on your family, decreasing your brother’s kid’s chances of survival. Probably better if you kick it for their sakes then.

Course, at what point you can say that your case is hopeless and other people are better off without you strikes me as very difficult to determine, especially since as social creatures we could in the above situation help out our brother’s kid’s by getting food/fighting off beats/ etc. Also, plenty of people who already have kids/ SOs/ contribute of their family’s survival, etc. commit suicide as well, so I’m not saying this is some sort of adaptive explanation for suicide, I’m just thinking out a case where it could be better for your genes for you to kill yourself, even if you’re still of reproductive age.

As for the Lynch paper, I’m about halfway through it, and am finding it veeery interesting, though as Scott points out, I’m not aware of any sort of objective measurement for complexity (though I think we can safely objectively state that say, the tobacco mosaic virus is less complex than a pony). Cells by themselves are incredibly complex (note: all I know about cells I know from Biol200), so how much more complex, in the scheme of things, are eukaryotes and multicellular creatures? Also, why does this paper mention intelligent design every other page?

Finally, as an example of ‘things that look uber-complex but probably aren’t’ and some unicellular complexity, here’s a podcast I was listening to today about slime mold: http://www.cbc.ca/quirks/archives/09-10/qq-2010-01-23.html (scroll down to Taking Directions from Slime Mould, it also links to the original Science paper among a bunch of other things).

Categories
Uncategorized

History is Strong

So to recap last week in a nutshell: we went over Phylogeny and Evolutionary Psychology, as well as Chainmail Bikinis.

Now for some musings:

Wayne Maddison’s talk on the pheneticist’s pessimism that it was impossible to reconstuct the tree of all biodiverity reminded me of a similar pessimism in Anthropology.

This pessimism is what led to “Salvage Anthropology,” the idea of recording all the variance before it “disappeared.” Cultures were static entities that needed saving or else they would go extinct. Now we look back and laugh at the idea of cultures dying, unless you are someone who has suffered from this pessimism and want your culture back.

During the early 20th century, when Social Darwinism and the idea of Unilinear Evolution was at its highest, Frans Boas was critiqued for studying his “Historical Particularism,” which is that not all effects have the same causes–we ought to examine particular case studies and history to understand how a particular society came to be as it is, not assume all societies were at different stages which culminated at Victorian Civilization (and the end of History, or Utopia, if you will).  Boas disliked generalizations (based on cherry-picking evidence to support an already established assumption) but his opposition thought that if you were to study all the case histories in the world, that everyone has their own (proximate?) reasons for doing things, it would be ultimately atheoretical–there was nothing to reveal, no overarching insight to be gained. What was the point of having a large collection of descriptions if you did no comparison work? How does that answer the big questions?

I think you need both generalizations and support from particulars: theory has to be grounded. There is nothing more practical than a good, working theory.

Categories
Uncategorized

MURC + proposal info

Here’s the MURC webpage including instructions for the conference, as well as the dates and deadlines, including workshop times.

The proposal description is pretty short and vague though, and I can’t find further details, so we’d probably have to wait until the workshop to polish it up. However, they do have a copy of last year’s MURC program with abstracts for some ideas. Note that the format did change a little, but until we get more info from the workshop, let’s just aim for something like those.

Feel free t0 use the comments for some brainstorming/testing ideas/discussion etc.

Categories
Extra readings language

ME TARZAN – Simple language morphology as a feature of large cross-cultural language communities

Have you ever wondered why English seems so simple compared to some other languages, particularly those notious for complex grammar like Russian or German? Have you wondered whether there was any reason why the local languages are so complex and filled with intricate grammar?

May I interest you in a very fresh awesome paper from PLoS ONE:

Language Structure Is Partly Determined by Social Structure Lupyan & Dale 2010 (open access; that is, no VPN required. Also, do support Open Access whenever possible! =D Publically-funded research must be made accessible to the public!)

They examined 2236(!) languages and looked for correlation between their morphological complexity and the ‘linguistic niche’ — whether the language is spoken over a vast area mostly by strangers, or used within a small tightly-knit community. The majority of the world’s languages are ‘esoteric’ (smaller population, fewer neighbouring languages, smaller area; eg. Tatar, Piraha, Ju|’hoan, Nuu-chah-nulth), contrary to what is most obvious to us, ie the ‘exoteric’ languages like English or Swahili. One would expect that the use of an exoteric language as a lingua franca may result in some changes in its structure, as its ‘purpose’ or ‘function’, if you will, is quite different. Anyway, they found that:

Continue reading “ME TARZAN – Simple language morphology as a feature of large cross-cultural language communities”

Spam prevention powered by Akismet