Pacifica (autumnwinds) wrote,
Pacifica
autumnwinds

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I am stuck.

After my committee meeting a few weeks ago, we established that I had done enough lab work. However, one member wanted me to take my data and do some in-depth computer analysis with it...nested clade, parsimony with varying gap weights and extension costs, coalescent analysis, etc. Fine.

The problem is, after I spent a lot of time going back over all my sequences to confirm if polymorphisms were real or mistaken basecalls, I established that there were no polymorphisms save the one 17 bp insertion present in about 60% of my samples. You either have the mutation or you don't. My data is virtually binary.

This makes analyses like nested clade or parsimony useless. The data just isn't complex enough to analyze.

I met with the committee member last week. He told me to go to GenBank and download lots of sequences for other plant families at the same locus and align them, to put my species in a phylogenetic context. Uh, okay, but it's been done. I already know where Alnus rubra resides in the plant kingdom.

Well, apart from the fact that it's not possible to get reliable conclusions from a single locus anyway, it turns out this particular locus (non-coding junk DNA) evolves fast enough that the alignment was basically gibberish. It's better for establishing population-level differences, which is why I picked it. There weren't enough similarities between the sequences to have the alignment make sense, even after a week of poking it with Sequencher and ClustalW.

So then my advisor suggests doing it at the more conserved locus of 18S. Which is fine, except I have to download all new sequences (including Alnus rubra, since I didn't sequence at this locus and therefore I'm not even using my own data). I did that all this weekend, although I had to spend time today downloading and sorting more because of length problems.

The thing is, I don't know where I'm going with this. This doesn't address any of my project objectives, it doesn't use any of my own data, and it's not going to establish anything that isn't already known and better-researched. I am so scared right now, because this is the first time in my project that I haven't had concrete goals and stopping points. I'm just floating. I think that because my data turned out to be simpler than anyone anticipated, they are making up work for me to do to make my project more publishable.

All I want to do is sit down, write my thesis, hand it in, and graduate. But as long as my committee is thinking up more busywork for me, I'll be stuck here. I don't have the slightest clue of when they'll let me go. Tyler's leaving for his summer job in a few weeks, everyone else will graduate, and I will be stuck here, doing nothing important, coming to no conclusions. I am trapped on the technical whims of two phylogeneticists and it terrifies me.
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