I've started using Papers to complement EndNote for keeping track of research papers that I've read. Think iPhoto for papers. In the past I've manually named papers that I've downloaded and tried to file them away. Except folders aren't very good metadata containers, because a paper will often need multiple tags. Papers handles all of the metadata for you and stores the files away on your disk. It has a built-in fulls screen view and uses PubMed to lookup random PDF files that you give it.

Why not just use EndNote? Its interface, file management and metadata capabilities are like a blast from the past circa MacOS 9. The programmers have probably been too busy rolling around in their money to actually make it decent.

Papers still needs some work though. It can't export to Word, which is why I still use both Papers and EndNote. It would be nice if it automatically pulled the paper title and looked it up in PubMed for you for identification. Speaking of which, they should hook it up with something like Google Scholar that is used by everyone. PubMed is pretty broad but definitely isn't used by the math and physics people. So Papers shows some promise and I'm using it for about 75% of my needs right now so stay tuned.

I've been brewing beer on a very irregular basis since the summer of 2002 and have made 7 batches thus far. Everything that I've learned has been based upon a few used books, friends and family and keeping meticulous records.

Why Brew Beer?

Jordan and I started brewing beer for two reasons. First, we had just graduated from high school and were not of legal drinking age yet. Second, good beer is expensive. A 12-pack of Sierra Nevada will set you back about the same amount in dollars and brewing seemed like a reasonable way to make any flavor of beer for the price of Pabst Blue Ribbon.

A more recent motivation to learn more about the basic processes involved is that (Saccharomyces cerevisiae) is the probably most intensely studied eucaryotic cell in history. It's genome composed of about 6000 genes was completely mapped in 1997 and there is plenty of information out there. There's also plenty of information about the yeast life cycle and ideal growth conditions. Brewing beer is just a practical application of insanely complicated biochemistry to create a tasty beverage and reduce your chance of scurvy.

Fermentation Temperature Control

Bottling

Bottling has a much lower initial cost and time investment than kegging, however it will quickly become apparent that the investment in a good kegging system will pay for itself very quickly. Between the 2-4 hours required to setup and bottle 5 gallons of beer and the ongoing cost of replacement bottles for the ones that grew all kinds of interesting things, kegging is cheaper in the long run.

With that said, you will need the following to bottle one 5-gallon batch of homebrew:

• (60) Relatively clean 12 oz. glass bottles (no screw-on caps)
• (60) Bottle caps
• (1) Hand-held bottle capper
• (1) Beer filled glass carboy
• (8 feet) 1/4" ID clear hose
• (1) Bottling Tube
• (1) Bottle scrubbing brush
• (1 cup) Corn sugar

1. Make the priming solution
   • Bring the corn sugar and 16 ounces of water to a boil. Stir until the sugar is dissolved. Cover, remove from heat and let cool until needed again.
2. Sanitize the bottles, caps, bottling tube and clear hose
   • Fill a sink with cold water and iodine cleaning solution per the instructions on the bottle
   • Quickly scrub the insides of the bottles with your scrubbing brush to remove any grime
   • Place them upside down on paper towels and allow to dry as long as possible.
3. Prepare for bottling
   • Place the carboy on a very high surface to generate enough surface for racking to the bottles.
   • Add the priming solution to the carboy. It will diffuse fairly uniformly by the time that you fill the bottles.
   • Place the clear tube in the carboy and lower to within 1-2" of the yeast sediment line
   • Attach the bottling tube to the clear hose, hold it above the carboy. Insert the valve side into your mouth and press with your tongue. Suck until enough beer is in the tube to start a siphon
   • Gather as many bottles as is convenient on the ground for easy access. Sit with them.
4. Bottle!
   • Press the bottling tube to the bottom of a bottle and fill until the beer is at the very top of the bottle. The displacement of the bottling tube will correct the apparent fill level (Be sure to fill the bottles with enough beer, or else there will be excess oxygen in the bottles that will allow hearty aerobic bacteria to grow quickly and take over your beer more quickly than normal)
   • Bottle until all of the bottles are full or you run out of beer. Don't be afraid to leave a small amount of good beer in the carboy to minimize the amount of yeast that ends up in each bottle.
5. Cap!
   • Carefully place the bottle caps on all of your bottles and then cap them. Once you get the technique down it should go fairly quickly.

Kegs

Keeping it cold: Building a kegerator on the cheap.

to be continued...

Our friend Andrew performed the ceremony at our wedding. We wrote up the script together beforehand while he was in L.A. and we were in Mountain View using Writely. We wanted something to the point and the ceremony lasted about 7 minutes I think. Without further ado, here's the script:

Introduction

Minister: Dearly beloved, we are gathered here together today to join together this man and this woman in holy matrimony. We are here to celebrate their union and to honor their commitment to one another. Today, Joey and Cassie proclaim their love to the world and we rejoice with them.

In marriage, we give ourselves freely and generously into the hands of the one we love, and in doing so, each of us receives the love and trust of the other as our most precious gift. But even as that gift is shared by two people who are in love, it also touches the friends and family members who in various ways support and contribute to the relationship. All of you are Joey's and Cassie’s community, and each of you has played some part in bringing them to this moment. This is why gathering as a community is such an important part of a wedding ceremony. Joseph and Cassandra are now taking a new form as a married couple, and in this form, they become part of our community in a new way.

I'm proud to say that i am part of Joey and Cassie's community, and have had the privilege of witnessing these two interact over the last three years. From the beginning it was evident that their relationship was somehow different than those of their peers; something about how they looked at each other, or the care and compassion that they showed for each other from the very beginning.

I recall one particular incident when the three of us were driving in a car together. It was after their second year in college and summer was just beginning. Cassie was moving to her new apartment, and we were helping her move. I asked, why aren't you living together? It seemed like an obvious question. They both looked at each other and didn't have an answer for me. It seemed like they just hadn't thought about it. At that point, it was already obvious to me and probably many of you that they were meant for each other. And sure enough, they moved in together one year later. the following year they went to Yosemite for Cassie's birthday and returned newly engaged. Hearing of their engagment was much the same as hearing that they had moved in together, it just seemed like it was inevitable

A vast, unknown future stretches out before you. The future, with its hopes and disappointments, its joys and its sorrows, is hidden from your eyes. But it is a great tribute to your belief in each other that you are willing to face those uncertainties together. May the pure, simple love with which you join hearts and hands today never fail, but grow deeper and surer with every year you spend together.

The Marriage Vows

Joseph and Cassandra, we are here to remember and rejoice with you and to recount with one another that it is love that guides us on our path, and to celebrate as you begin this journey together. It is in this spirit that you have come here to today to exchange these vows.

Minister: (To the groom) Joseph, do you take this woman to be thy wedded wife? To have and to hold from this day forward, for better or for worse, for richer, for poorer, in sickness and in health, to love and to cherish; from this day on so long as you both shall live?

Groom: I do.

Minister: (To the bride) Cassandra, do you take this man to be thy wedded husband? To have and to hold from this day forward, for better or for worse, for richer, for poorer, in sickness and in health, to love and to cherish; from this day on so long as you both shall live?

Bride: I do.

The Rings

Minister: The wedding ring is an unbroken circle symbolizing unending and everlasting love.

Joseph, have you a token of your love for Cassandra?

(Ameet hands Joey the ring)

Minister: Cassandra, have you a token of your love for Joseph?

(Mandy hands Cassie the ring)

Minister: Traditionally, the passage to the status of husband and wife is marked by the exchange of rings. These rings are a symbol of the unbroken circle of love. Love freely given has no beginning and no end. Love freely given has no giver and no receiver - for each is the giver and each is the receiver. May these rings remind you always of the vows you have taken here today.

Minister: Joseph place this ring on Cassandra's finger and repeat after me:

This ring, a gift for you, symbolizes my desire that you be my wife from this day forward.

Groom: (repeats)

Minister: Cassandra place this ring on Joseph's finger and repeat after me:
This ring, a gift for you, symbolizes my wish that you be my husband from this day forward.

Bride: (repeats)

Ending

Minister: Joseph and Casssandra, you have given and pledged your promises to each other, and have declared your everlasting love by giving and receiving rings. By the authority vested in me by the State of California, I now pronounce you husband and wife.

(To the groom) You may kiss the bride.

(cheering)

Minister: Ladies and Gentlemen, I present to you Mr. and Mrs. Joseph Carl Doll.

What is Dogully you ask?

Dogully is a type of lake. One that is filled with huge seacreatures that are called bobs. These bobs are very dangerous. You have probably seen a Dogully without even knowing it, especially if you know Joey or Cassie personally.

Speculations are abound. Here are just a few that we've received via email:

• My brother was eaten by a bob. I'll never be the same. I'm so cold... please hold me.
• You know the chocolate river in Willy Wonka? It's nothing like that, but it would be awesome to go swimming in there.

Where'd the logo come from?

The tree is located in Dillon Beach, CA and you will see it right by the last bit of road as you are heading to the beach. I took a photo of it some time ago and a few years later Cassie got me to stick it in Illustrator and trace it. Four versions of the tree ended up on my last site, The Lost Coast, and the autumn tree was my favorite, so it ended up here.

(Update: The tree is no longer here but can be found at my school site)

Here are old archived versions as my website has developed over the years.

• Go Banana!
• The Lost Coast

Flea Medicine

The flea medicine business is kind've funny. Medicine for your 10 pound cat costs as much as for your 150 pound wildabeast even though the only difference is the volume of the dose. Here's the info on Frontline plus for the dog medicine.

So what we do is buy the big dog dose, transfer it to a small glass bottle and store it in the fridge. When it's time to give the cats their medicine we use a syringe (no needle!) to dispense the medicine. For two cats at 0.5 ml per dose, 4.5 ml will last 5 months, so you're talking about $1 per dose rather than $10 per dose.

Costs/Reviews

Our cat sherlock had an endoscopy to remove a needle that he swallowed. It was performed in Capitola, CA at Pacific Veterinary Specialists Emergency Services on a Saturday night and cost about $1000.

In July 2007 Sherlock started having trouble urinating and we saw that he had blood in his urine. We took him to Adobe Pet Hospital because they were nearby and had drop-in appointments. They had to insert a catheter and kept him for two nights. The overall cost was about $1300. Overall it was pretty poor service and it didn't seem like the veterinarians or staff cared about how our cat did. It was in stark contrast with our previous encounter at PVES (see above). I wouldn't go there again.

Later in July, Sherlock had serious trouble going to the bathroom again. They weren't able to get the catheter in because it was so clogged, so he ended up going into surgery (perineal urethrostomy) to open up his urethra. The surgery went great and he has been doing really well since. It was expensive, but it worked out to be close to the same cost of the prior hospital stays when he had to have a catheter (~$3000) and the fact that he can go to the bathroom is infinitely worth it.

Doggy Daycare

We take Lola (our dog) to Klub K9 Pet Center in Sunnyvale and highly recommend it. It's a little over $20/day if you buy a 20-pack, otherwise it's about $40 per day. Their staff is great, they have four huge play areas for the dogs, and they do cage-free boarding.

Joey's Books

I keep track of the books I've read at aNobii, which I highly recommend. The short stuff is just below.

Shorts

Interviews, short articles and speeches that I have found particularly insightful.

•  You and Your Researce Richard Hamming, Talk from 1986. Read in November 2005.
  • Interesting perspectives about how good science is performed and why you should do what you love.
• Applying to Ph.D. Programs in Computer Science Mor Harchol-Balter, 2003. Read in November 2005.
  • If you are thinking about going to graduate school you should really read this. It is a great help.
• Applying for Fellowships and then some Philip Guo, 2006. Read in December 2006.
  • Various writings about graduate school and applying to them from a PhD student.
• Cargo Cult Science Richard Feynman, 1974. Read in January 2006.
  • Why bad science is done and how our expectations can cloud results.
• Steve Jobs commencement at Stanford in 2005. Read in January 2006.
• An interview with Steven Chu
  • The integrated circuit, optical optical trap, and probably many others were both discovered when everyone went away from the office for one reason or another. Weird.

Cassie's Books

I'm not as good as Joey about keeping this up to date (also on aNobii), but the books below are ones that I have been working on.

• David Allen's Getting Things Done
  • This book is very informative. It's all about getting all the things you need to do in your life out of your head and on to paper. Although it is written for middle aged businessmen, it has a lot of good ideas about how to make your life more organized. It was definitely a good read and helped both Joey and I become much more productive.
• Robert Jordan's ''The Wheel of Time'' series
  • This series is incredibly addicting. It's sci-fi, 12 books long. He passed away recently but the final book is in the works.
• Christopher Paolini's Eragon'' and Eldest
  • Much better than the movie leads you to believe
• Orson Scott Card's Wyrms
  • A lot like Ender's Game but a little heavier on the religion. I think it is one of his best
• Lots and lots of girly books

* 20 Pears
* 128 oz. Cranberry Juice
* 10 tbsp Sugar
* 1 tsp Cinnamon
* 1 tsp Cloves

Peel, core and halve pears lengthwise. In a medium size saucepan, combine all the ingredients; bring to a boil. Reduce heat and simmer, covered, for 15 minutes or until pears are tender. This can be served warm over pancakes or waffles.

From Nick Wong's kitchen.

Ingredients

*1 cup milk
*1 cup water
*1/2 pound butter
*1/8 teaspoon salt
*2 cups flour
*8 eggs

Instructions

#Combine milk, water, salt and butter in pot.
#Heat until butter melts, then bring to a boil - do not let water reduce.
#Remove from heat and add flour all at once.
#Stir *very* fast with a wooden spoon and get all the lumps out.
#When smooth, return to heat and cook for one minute on low heat, stirring with spoon. The ough should be able to roll around when the pot is shaken. A nutty smell means it's done.
#Let dough cool off, until just warm to the touch.
#Add eggs two at a time, beating slowly until dough is homogeneous after every addition. (You're looking for a smooth, shiny texture, and you may not need all the eggs)
#Pipe out the dough onto parchment-lined sheets
#Bake at 400F for 20 minutes, reduce to 350F and bake 10 more minutes. (They should look golden brown)
#As baked dough is cooling, leave it in the oven with the door slightly open to remove any of the remaining water still in the dough

From Nick Wong's kitchen.

Ingredients

*1 teaspoon unflavored gelatin
*1 cup half and half
*3 tablespoon sugar
*1/2 teaspoon vanilla extract

Instructions

#Soften gelatin in 1 tablespoon cold water
#Heat sugar and half and half in pot until sugar is dissolved
#Whisk in gelatin and vanilla extract
#Pour into glass containers, cover with plastic wrap, and chill for at least 2 hours.

*To get the panna cotta out of the containers, you can dip the containers into hot water for 30 seconds and gently shake them out. Or, you can just eat them straight out of the containers.

*To make chocolate panna cotta, you can add a tablespoon of cocoa into the sugar/half and half mixture, adding more depending on how chocolatey you want it.

(We made this one up, it's a work in progress)* 3 boneless skinless chicken breasts
* mozzarella cheese
* garlic salt or minced garlic
* italian seasoning
* onion powder
* tomato sauce/paste
* 1/2 cup flour
* 3 tablespoons vegetable oil

In a bowl, combine some of the mozzarella cheese, the garlic, italian seasoning, a tiny bit of sauce/paste and onion powder. Mix well.

Cut pockets into the chicken breasts so that the hole is only open on one side. Stuff the chicken with the mozzarella cheese mixture.

Preheat oven to 350 degrees F (175 degrees C).

Coat the chicken with flour. In a large skillet, heat the oil and brown the chicken over medium high heat. Transfer to a baking dish.

Pour remaining tomato sauce and spices over chicken. Top chicken with additional mozzarella cheese. Cover and bake in the preheated oven for 30 minutes. Remove cover and bake for 10 minutes more. Let cool and serve.