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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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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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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).

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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.

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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.

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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:

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test post

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Week 2

Of language acquisition, phylogeny and development

First off, a brief summary of week 2:

– Greg Bole gave us a great introduction to evolutionary biology focusing on replicators,defining the latter as a ‘stable pattern that can replicate itself’ (well-said, I think!); this opens up a wide territory for exploring what constitutes a replicator and how it applies outside biology.

– We also discussed levels of selection, more or less agreeing that the basic level of explanation should be on the gene (or, to generalise, replicator?) level; a higher level of organisation can be evoked in cases where gene-centred explanations fail (need specific examples; group selection to be discussed in more detail later)

– Fundamentals of biological evolution (molecular, and a touch of population genetics) were discussed very briefly, to give an idea of how evolution actually physically works in biology. Molecular (incl neutral) evolution will be covered in greater detail later; speciation and some population biology should be discussed tomorrow; but it would be nice to learn a little more about the mechanics of selection (population genetics stuff, etc), as I, for one, am absolutely clueless in that field*.

* This may be hard to believe, but there was for a long time (and still lingers) this divide between botanists and zoologists. This divide did not just happen on a taxonomic level — the approaches to evolutionary biology were fundamentally different in the two disciplines! Zoologists tend to focus more on speciation, selection, etc; ie. the actual mechanisms of how species diverge with a very population-based approach. Botanists, on the other hand, are obsessed with phylogenies and have a greater inclination to play with molecular evolution. It’s quite hilarious how the disciplines are all influenced tremendously by their histories, and this does have an impact on how we view and understand certain subjects!

This week, we should get a thorough grasp on phylogenies, focusing on how to read them correctly, but also something about how they’re made and what they actually mean. Some vile misconceptions (eg. the wretched progressive ‘ladder’ view of evolution) shall be ruthlessly despensed with. On Thursday, we should discuss the psychology paper, and spend the remaining time brainstorming some project ideas for the proposal due next week. (I’m as worried as you guys are, despite having known about this months ago…! Still have no idea/too many ideas for a topic…both simultaneously, somehow…)

And now, a response to Scott’s post on language and phylogenies: (too long to post as a comment…)

For one thing, phylogenies actually originated in linguistics. But perhaps what you mean is, do all languages fit on a single nice phylogeny? It’s interesting that you bring up creoles and pidgins — I find that example simply fascinating, and almost took language acquisition (LING452 methinks), except that it would’ve been a bit much that term. I guess a biological analogue to language learning/acquisition could be embryonic development:

It may help to think of languages as mature organisms, including genetics, epigenetics and various stuff that happened to them during their own lifetime. Some of that stuff is clearly inherited, some is murky, some has little influence on the progeny (among animals the example would be losing a limb). So, by analogy, one’s personal language* would also have some traits that are heritable, and some that are not. The language is still recogniseable as a ‘species’, if you will, but has some idiosyncratic streaks to it.

*One unfortunate thing is that Chomsky, who pretty much ruled the field of linguistics for decades, didn’t care much for individual variation within a language, and focused on the ‘pure’ language (or dialect) itself. Some linguists today are beginning to realise that was not such a good idea…

Now, in the case of pidgins and creoles, a pidgin would be sort of like mashing various parts of mature biological organisms together. This is seldom possible in the biological world, not spontaneously anyway. I say ‘seldom’ because things like grafting of both plants and some single cell organisms can generate these weird chimaeric hybrids. In the case of single celled organisms, this could actually be somewhat heritable, via cellular inheritance. But that’s murky ground. So biological ‘pidgins’ could be possible.

Creoles, on the other hand, are like mashing various parts of a mature biological organism together AND creating a whole new stable lineage that way. The gut reaction would be to call that ridiculous, but…luckily for us, biology is about as messy as linguistics, if not more so. Endosymbiosis is one complication where you actually get gene transfer between genomes, and the chimaeric organisms persist (there’s some stunningly complex stories out there, such as an organism with 6 different extant genome compartments (nuclei, plastids, mitochondria); in land plants we have cases of hybridisation between closely related species. The endosymbiosis case may be somewhat VERY LOOSELY analogous to creolisation, as we have multiple unrelated genomes and cells working in a single compartment, forming a single organism. It may be a stretch though.

Next up: what is an organism? =D

By the way, in April, Ford Doolittle (Dalhousie)  is giving a talk at the biodiversity research seminar (about constructive neutral evolution AFAIK); he’s a major MAJOR oponent of the bacterial tree; that is, he argues that because of all the lateral gene transfer (ie, between lineages rather than down along them), the tree concept fails for bacteria. It’s a long raging war, and if you guys are interested we could explore it. But in any case, closer to the day (it’s end of April, if I recall) I can remind you guys again, and highly recommend his talk. Afterwards, if there’s time, perhaps you could even pester him about LGT and the tree of life stuff.

Sorry for the really long post…

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Week 2 Weekly Posts

Okay, here’s my contribution to the week. We spoke a bit about levels of selection, so I thought I’d throw up a paper that shows where an individual’s interest is counter to a group’s interest. There’s also a bit about sex in there, which might be useful to start thinking about now. The paper is How to go extinct by mating too much: population consequences of male mate choice and efficiency n a sexual-asexual species complex by Katja U. Heubel, Daniel J. Rankin and Hanna Kokko.  2009.

First a bit of background, there’s this guppy-like fish genus called Poecilia. In several of the species in that genus, when they interbreed their offspring are these things called gynogens. They’re always female, and their offspring are clones. But while each egg they produce contains all the genetic material their offspring need, they still need to have the egg come into contact with sperm from one of the parental species to jump start the egg’s development. So, the gynogen species need to live around parental species to get the sperm off the males. Males theoretically get no benefit from fertilizing one of these eggs, since their genetic material isn’t passed on in the offspring (though one study found that females of the male’s species are more likely to mate with him if they see him having sex with one of gynogens. This puzzles everyone). This makes gynogens effectively sperm parasitizers.

What’s the problem here? Well the asexual fish should be able to produce twice the number of offspring as the sexual fish, since asexuals only need one individual of their own species to produce another, and sexual species need two individuals (this is officially called the ‘two fold cost of sex’). Thus, the gynogens should increase their population size much faster than the sexual species living in the same area, and should end up out-competing the sexual species for males by sheer numbers.  This causes the sexual species to go extinct, and then the asexual species soon follows because it no longer has any males to get sperm off of.

Two possible factors might throw this off: If males produce enough sperm, they should be able to fertilize all the females, sexual and asexual, and both lineages should persist. Or, males  might preferentially mate with their own species. These traits aren’t necessarily good for an individual to evolve though – sperm is costly to produce, and if the male is too discriminating, it might accidently pass up a chance to mate with a female of its own species, or waste too much time trying to tell whether a potential mate is a gynogen or not (these fish look very similar). The paper looked at these two traits, and constructed a model to see what levels of these traits would be best for the population as a whole (in other words, what amounts of male discrimination and sperm production combined lead to the long-term survival of the species?). They then compared the expected rates to rates in the wild.

I’ll spare the math because well, it’s mathy, and I’ve written a novel already. But, they found that their predicted numbers, and numbers observed in most gynogen populations didn’t match up. They pointed out that local populations have been observed to go extinct, and also that these fish are good colonizers, so as long as the extinction rate is low, individuals might ‘escape’ by colonizing a new area, and the whole game would play out over again. There’s quite a few other factors to consider with these fish (one being that the asexual species don’t completely overlap in niche with the sexual species, which would lessen a lot of competition), but I thought this example was interesting because it talked about group selection, and because gynogens are friggin weird and awesome.

For further reading about asexual fish (and uh, other vertebrates) I suggest Clonality by John Avise. It’s in Woodward. 🙂

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language Week 2

Re: Scott’s post about linguistic phylogeny

I tried to simply reply to the post itself, but I encountered the same “you must be logged in” glitch as previously complained about. What’s mysterious is that for some posts I am logged in, and for others I am not.

In any case, I think that a human population’s capacity to create a new grammar when one is lacking or unavailable does not exclude language from an evolutionary model. Specifically, I am thinking of the way that linguistic information is inherited from previous generations with astounding fidelity. And then mistakes are made in the copying process or populations migrate or whatever and the next thing you know, you have a dialect, then a new language altogether. This looks an awful lot like speciation to me.

It’s also important to remember that although an analogy may not fit to the letter, that doesn’t mean it isn’t still useful. While it would be brilliant if language evolved in literally the same way as genetic material, that would also be way too simple and make our lives far too easy. If you accept such a model as analogous and account for discrepancies therein, you can discover more about both subjects through their differences, and perhaps modify your understanding of them (hopefully in a useful way).

Switching gears completely, the Maddison reading for tomorrow made me wonder what speciation looks like. Is there a concrete example of this that has been observed? At what point do species split–that is, when can we start naming them in Latin? Can they only split in two directions, or can they branch off in three directions at once?

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