A random bag of music, part I

Welcome to A Random Bag of Music- the first installment. This is just a place where I can randomly list (oxymoron?) some favorite songs/albums/artists and talk about them a bit. I’m going to number the entries for clarity, but there is no order. It’s like asking me what’s my favorite color- really? I like all colors for different purposes, in different moods, at different times, in different shades- there’s no favorite. Same thing with music (though a bit more stratified- there’s definitely genres of music that I care for less and more). Anyway, here goes. I’d be happy for any comments pointing me to more like these- or just whatever you like. These are a few from awhile back. I’ll post more current stuff in the next installment.

1. John Vanderslice, “You Were my Fiji”. This gem is a haiku of love and loss (no, I know it’s not REALLY a haiku- it’s just short and to the point). I’ve worked up a version of it that I sing and play that I’ll post here sometime when I get it together. This live version isn’t as good as the studio version IMHO, but it gives the idea. To me it captures a brief, simple love affair that has lasted in the singer’s mind as a shining moment, even though he had to leave and go on the road.

2. The Mountaingoats, “No Children”. The most amazingly hopeful depressing song about a bad relationship EVER. This song is full of so many great lines and so upbeat in the way it’s sung and so depressing in the lyrics. The amazing thing is that the song is all about hope. The singer hopes about many things and it’s clear that even though he’s miserable he wants to be in the situation in some way and he’s aligned with his partner in misery. It’s a very odd song, but I recognize the feeling of being so entangled with someone that is so bad for you that you can’t see beyond them and you together, even though you hope to.

3. Built To Spill, anything off of “Keep it Like A Secret” or “Perfect From Now On”. Possibly my two favorite albums of all time. This was when I realized the true nature of shoegazer rock. But that’s really selling it short. The soaring guitars, the building jams, the interesting and sometimes inscrutable lyrics. This is the pinnacle. I probably listened to these two albums more than any others while finishing up my graduate thesis (with the possible exception of the next entry). Here’s the lead-off song on Keep It Like Secret, which I currently have as the wake-up song on my cell phone. One of the comments on this YouTube video, “The best part starts at 0:00”. Agreed.

4. Modest Mouse, “The Lonesome Crowded West”. Where do I start with this album. It’s gritty, hooky, weird… and connects on some level that I don’t quite understand. Most of the songs on this album are great, but some take a little breaking in (like, listening to them over and over). I’ll point out Teeth Like God’s Shoeshine because for the life of me I don’t really know what its _about_ but it is very familiar territory somehow. “The malls are the soon to be ghost towns, well so-long, farewell, goodbye. Let’s all have another orange julius, thick syrup standing in lines.”

That’s all for now! The first two songs I’ve worked out my own (very, very rudimentary) versions of that I’ll post soon. It should be an interesting contrast.

Garlic Ginger Butternut Spice Soup- My First Food Blog!

Garlic Ginger Butternut Spice Soup

So we planted a medium-sized garden and had a great harvest of several things, tomatoes, cucumbers, basil, and butternut squash. I was looking for a recipe for a savory and satisfying butternut squash soup recipe on the internet and couldn’t seem to find

Our garden 2012

Bella and Naveen outstanding in their field

anything that looked that great. Then today I was organizing some old files on my computer and realized that I’d actually come up with a recipe two years ago when we also had a good butternut squash crop. What a find! This soup has enough body to be very satisfying and spices to keep it interesting. Plus a bunch of garlic and a bit of sweetness and you have a wonderful soup that will make you feel good to your core when the cold winds start to blow. I modified it slightly from my previous recipe by substituting non-fat greek yogurt and milk for the heavy cream, adding the fresh ginger, and some dried orange rind I saw and thought would go well in the soup (it does). Next time I’m going to try to reduce the fat and calories a bit by dropping the olive oil to 1 Tbs and the butter to 2. But this is still pretty healthy (see below for nutrition).

The Recipe- makes about 9 cups

Alien Mary (Green Tomato Bloody Mary)

I enjoyed making this soup with another garden favorite: my own Alien Mary (green tomato bloody mary). I’ll post a recipe for this in the future.

2 medium or 1 large butternut squash, about 2 pounds

3 tablespoons butter

2 tablespoons olive oil

10-15 whole sage leaves

10-20 cloves garlic minced

1/3 cup non-fat strained greek yogurt (like Fage’ brand)

2/3 cup non-fat milk

32 oz chicken broth

1.5 T Worcestershire sauce

3 T balsamic vinegar

½ t ground nutmeg

½ t ground coriander

¼ t ground cinnamon

¼ t ground cloves

¼ t ground cinnamon

1 t dried orange rind

1 Tbs fresh grated ginger

1 t kosher salt

3 T sugar

3 T maple syrup


1/3 cup cup pine nuts, lightly toasted

Dry Jack or Parmesan cheese

Salt and pepper to taste

1. Peel the squash, cut it one-half inch slices, toss with a little olive oil and salt, and roast in
Cubed squash a single layer in a 425 degree oven for 25-30 minutes, or until tender and brown. Set aside to cool.

2. When cooled, put slices of squash in a food processor and add some of the broth. Puree in 2-3 batches until smooth. You can also just use a stick blender to puree the squash after step 4 below and do it right in the pot. Much simpler that way and it blends the garlic and sage so they’re not lumpy in the soup.

Lots of garlic, sage and butter toasting up to yumminess

That’s a LOT of garlic right there.

3. In a large pot, over low heat, warm the butter, sage and garlic. Cook until garlic starts to brown. Don’t overcook garlic.

4. Add in the squash mixture, turn up heat to medium, and sauté for 2-3 minutes. Add remainder of the broth.

5. Add the cream, sugar, maple syrup, and the spices and slowly heat up just to a boil, then turn heat down. Add Worcestershire sauce and vinegar and mix. Finally add the fresh ginger. Stir the soup well and cook on low heat for 10 minutes to blend the flavors.

Finished soup

The soup has a warm brownish color. It’s not as yellow-orange as it could be because of the worcestershire sauce and basalmic vinegar that help give the soup it’s depth of flavor and savoriness.

6. Top each serving with sauce, pine nuts and thin shavings of cheese (a vegetable peeler works well for this) and a little cracked pepper, and serve immediately.

Nutrition information: 1 cup per serving (not counting garnish)

174 calories

27 g carbohydrates

7 g fat

4 g protein

Ta-da! Delicious bowl of soup with garnish.

Publication impact factor analysis

So here’s an interesting (to me) exercise I did in self-data-collection-and-analysis. I analyzed my publications from grad school and before (at OHSU), from my post-doc (at UW), and from my current scientist position (at PNNL). I determined the number of times each article had been cited by another publication per year, which is the Impact Factor of the article and plotted that versus the Impact Factor for the journal that the article was published in, which is the same idea only averaged over all the articles published in that journal. Here’s the plot I came up with:

On the X axis is the reported Impact Factor (IF) of the journal and on the Y axis is the Impact Factor of the article I published (mean number of citations by other papers per year) according to Google Scholar. The colors indicate the institute where I was at when I published the papers.

This is interesting because it seems to show a couple trends. First is that it looks like all my publications from post-doc and my current position outdo the journal impact factor by 3.8x and 2.4x, respectively. That’s a good thing I think. The other is that my grad school publications do worse than the journal’s IF. This could be because of their age since papers hit a peak of ‘relevance’ when they are cited most, then taper off when they are supplanted by more current references. Not sure.

The one outlier is a paper that I worked on to analyze the genome of Oryza sativa, rice. It has a pretty large citation record, but I was interested to see what the trends would look like without it in the picture. Removing that point I got:

On the X axis is the reported Impact Factor (IF) of the journal and on the Y axis is the Impact Factor of the article I published (mean number of citations by other papers per year) according to Google Scholar. The colors indicate the institute where I was at when I published the papers. In this figure I’ve removed a high-impact outlier.

Now this seems to show that my current work is significantly outperforming my post-doc and grad school work by quite a bit. Again, not a bad thing I think. Also, in general I’m publishing in lower impact journals, but since I’m outperforming their impact factors maybe I should be shooting higher. I’ll send these plots along with my next submission to Nature. I think the editors will see it my way.

Free will or the lack thereof

Reposted from my facebook account http://www.facebook.com/jemworks

I’m interested in hearing people’s thoughts on this—

Thinking about pride.

If you’re proud of something you’ve done: an accomplishment, a decision you’ve made, how good your life is right now, how much money you’ve got, etc.

Think about why you’ve done what you’ve done. Essentially there are four reasons:

1. Your character because of how you were raised by your parents.

2. Your character because of your genetics from your parents.

3. Your character because of things that have happened to you over the years.

4. Your character because of ‘who you are’, your ‘soul’, your character that does not arise from factors 1-3


So, for factor 1 you have no control- you don’t get to pick your parents or decide how they might raise you.

Ditto for factor 2, maybe even more so.

For 3, any influences and random happenings that have shaped your life are, well, random, or planned by fate or a being that is not under your control.

The case of 4 is a bit more complicated. If you believe you are imbued with a ‘soul’ that allows you to ‘rise above’ or make decisions that may not be directly ascribed to factors 1-3, then that soul must arise from outside yourself, and therefore is not under your control. If you believe that you ‘are you’ simply because of ‘who you are’, then I refer you to factors 1-3 and ask what factors can arise that are outside of those three.


So then being proud of something you’ve accomplished is OK, but it’s good to know that it’s completly outside of your ‘control’ and you can’t actually take credit for anything. This is actually true of any decisions you make, regardless of whether you are proud of them or not. That is to say, free will, as is commonly envisioned, is not a concept that makes a lot of sense- it does not exist in the way that we usually think of it. We are not able to make decisions that are not directly attributable (in some sense) to some combination of factors 1-4.


Continuing this thread- this pointedly does not mean that people are not ‘responsible’ for their actions simply because there is no free will. Responsibility is a social construct and is very important to allow societies to function. That is, personal responsibility allows a society to regulate itself. For example, no one would argue that we should let serial killers go free because “it’s not really their fault”. It isn’t- they did not choose to become that way (they have to obey the no free will law as well), but they are significantly detrimental to society and thus must be controlled and held responsible for their actions. This is true of many other things and the extent to which you embrace this is one factor contributing to how conservative or liberal your beliefs are.