Genome

So I said below that sometimes I wish I were an ecologist, but genetic and molecular biology sure does get its perks. Maybe when I graduate I'll sign on with the new group to map the genome of the cocoa bean, which I'm sure would mean I'd get complimentary chocolate for life.

I was going to write a nice little essay on genomes and why you should all care about them, but I think I'll hold off on that for another day. This is enough science for one day- and I have things to do this afternoon. Debriefing will occur later.

Signing off.

Specifically speaking, but also in general

Every so often I wish I were an ecologist. I love my molecular and microbiology, but macrobiology is cool in a completely new way! Not only are scientists still discovering completely new species, but they are discovering completely new species that have amazing features like we've never seen before. Take, for example, this newly discovered frog that lives happily in the jungles of South America, just like all its other little frog relatives- except for the minor detail that all other frogs have lungs. This one doesn't. He survives, as far as we can tell, by absorbing oxygen through his skin. He lives in fast-moving streams, which is important because the speed of the water mixes more oxygen in, and essentially allows this frog to breathe underwater. I'm kind of jealous. Harry Potter probably could have used this ability in the Goblet of Fire, when he had to swim deep underwater. I bet he would have liked it better than growing gills.

So, back to the discovery of new species. It's a very exciting, and it never ceased to amaze me how much biodiversity there is on this planet. But it's always good to remember that the terms "species" and "genus" (along with its unusual plural "genera") are man-made devices to describe what we're seeing. Quite often, most animals and almost all plants go about their merry way, reproducing with whomever they like, even if they happen to be crossing the not-so-sacred boundaries of what humans have designated as different species. That's just how evolution is. It's more of a big, gradual shift in characteristics across the whole tree of life than it is concrete designations. But I think that kind of adds to the fun.

Also, bonus points if you can catch the pun in the title.

The adventures of an accidental scientst: part II

Sometime at the beginning of this year, a small lab was cleared out and turned into a room for the microscopes and microscope related equipment. Since I use microscopes a decent amount and most of the other kids in the lab do not, this became essentially my lab- mine and Dr. J's. It's pretty small, but it's kind of nice to have my own space. This is my light microscope, the more high-tech one:
After we got things kind of moved in, Dr. J left me a list of things to do on the whiteboard. After a couple of days, I noticed that someone had added to the list. Item 4 was not there originally:
Now, knowing the character who was responsible for this addition, I was not surprised at all and I rolled my eyes a little. A few days later, I noticed on Facebook that he had demanded brownies from another girl who used to be in our program.

Later in the semester, this announcement appeared on the whiteboard in the main lab:

When Dr. C saw it, he found a few pennies in his pocket to donate to the worthy cause. I assume he was hoping Jared would use them to go on a date and get rid of his status as a bachelor. Dr. M tried to convince Jared that I had spit in the bag, but fortunately that was not very believable.

What was believable was when this notice appeared on the lab whiteboard a while later:


Heh. Someone tried changing the greater than sign to be a less than sign, and erased the 5. But Jared, with his sharp acumen, noticed and changed it back. I have to hand it to him- he's persistent.

Also, to be fair, he's the only on who remembered my birthday in the lab, and even made brownies to bring up. He planned to take a special courier bag to campus instead of his backpack for easier brownie transportation. He got to campus, looked into the courier bag, and discovered that he had left the brownies at home. But we'll give him an "A" for effort.

The adventures of an accidental scientst: part I

Last night, I spent some time talking to a good friend who's studying to take the GRE, or graduate records exam, in preparation to go to grad school. He was a little concerned about his potential performance on the math section, since his math is a little rusty. In an effort to cheer him up, I told him how low my math score was on the GRE- a pretty low percentile. I don't feel like posting just how low it was. But, on the bright side, I scored in a very high percentile with my verbal part of the test. And my essays got one mark below a perfect score.

At this point in the conversation, we both realized that based on my GRE score, nobody would place me in the sciences for advanced study. In fact, I got comments about my scores when I spoke with professors from different schools about attending their programs. Fortunately, nobody saw fit to use my test score to prevent me from getting accepted to their program.

However, I've been thinking about it a bit today, and I really am a little surprised that I ended up studying science. I love it passionately, don't get me wrong. Anyone who's seen me give a presentation on my research or sub a class for a professor can attest that I get maybe even a little too excited about it (my little sisters probably have something to say about this, too, when they come to me for biology and chemistry homework help). But, I'm really a right-brained person. Numbers and other sciency things are not my forte. They're not even my mezzo-forte. Maybe a mezzo-piano.

Yet, here I am. Somehow I didn't wind up studying humanities, although I find the written word and studying languages and history fascinating. One of my guilty pleasures is reading dictionaries for fun to learn new words. I didn't end up in a music-based major, although I've pursued music as much as I could in college, playing my flute in the nonaudition groups and taking music lessons. Nope, I am a botanist and a geneticist. I assure you there was no pressure at home to pursue either of these majors.

So, I find myself to be something of an accidental scientist: I'm not completely sure how I got here, but I'm quite pleased to stay along for the ride. And so I bring you the first installment of The Adventures of an Accidental Scientist.

This introductory installment comes to you after some debate, but it's such a funny story that I have to share it.

A little background: in the lab, one of the most basic things we do is separate very small things (ie molecules) according to their size, shape, or charge. One of the most common things to separate by size in a genetics lab is pieces of DNA. We do this by putting the mixture of DNA into a large slab of something called agarose, which is essentially like really thick jell-o. You could eat it if you wanted to, but I don't recommend it. Gels come in powder form, just like jell-o, and you make one by pouring the powder into a buffer solution and heating it up and then pouring it in a gel box, which is also a lot like making jell-o. However, unlike jell-o, gels can be reused. We put them in Erlennmyer flasks in a big fridge in the lab until the next time we need a gel, and then one of them gets taken out, melted down, and recast:
Anyway, a lot of times it's necessary to run an agarose gel to see if different reactions worked or not. A few months ago, I was running a lot of gels and coming to dislike them strongly because each time I did so, I discovered that my reactions weren't working. I tried to take the approach of not shooting the messenger, but one day I'd had enough and I got rather hot and bothered with my little gel.

I picked it up and looked at it for a minute. Just then, my friend Ryan walked in to the room and could tell I was frustrated with the way my research was going. After he sympathized with me, I suddenly got an impish idea.

"Ryan," I said, "would it be terrible if I threw my gel at the wall to relieve stress?" Ryan laughed and then he realized that I meant it. So, being a gentleman, he replied that he didn't think it would be too bad, as long as none of the professors walked in right then. Also, it should be noted that gel gets on the floor all the time and nothing bad results.

Consequently, I took careful aim and chucked my gel at the wall. Well, not at the real wall, strictly speaking. I threw it at a large fume hood that happened to be in front of me.

What I wasn't counting on was the fact that the gel was very slippery and flew out of my hand at a much sharper angle than I intended. Thus, Ryan and I both watched in amazement as the gel arced up and landed gracefully on top of the fume hood, a good ten feet up. Then we both burst out laughing. The unintended result did more to relieve my stress than just chucking the gel would have.

Two months later, Ryan and I were both at work late in the evening, finishing some things up. It was probably after 9, and we were both ready to go home. As we waited for our reactions to finish, we suddenly thought of the gel I had thrown, and Ryan climbed up on the sink to see if he could see it on the fume hood. Lo and behold, it was still there! It had become completely dehydrated and was super thin and brittle by then. We got a good chuckle out of that.
Although hurling a gel at the wall was fun and provided much entertainment, I don't think I'll make a habit of it. It doesn't seem like good science somehow.

A little lift goes a long way

Once again, I assert that the value of good friends who sustain good relationships cannot be overrated. Their value is greater than that of any worldly wealth. Yay for siblings, roommates, and colleagues who have been my life preservers while I swim.

Perserverence

Sometimes life is hard. Really, really hard. Sometimes it's hard to see the forest for the trees. Sometimes, even when you know there's a light at the end of the tunnel, the tunnel is so long that you can't see the light. Sometimes the Lord lets the storm rage and just lets us swim to see how far we can get.
I hope I make it to dry land.

Happy Fathers' Day

It's interesting- the older I get, the more respect and love I have for my dad. He is a man of unbelievable patience, longsuffering, intelligence, and goofy humor. Life has not really dealt him an easy hand. But he has done amazing things with what he's been given.When I think of my dad, I think of:

- math help in junior high and high school. We all took it for granted that Dad would be there to help us figure out the wiles of algebra, trig, and calculus, and he was! Sometimes late into the night. And he never got fed up with us, even though I probably deserved it sometimes when it was 11 PM and I was pouting.

- Long, thoughtful discussion and discourses about the gospel during family scripture study. This was something I came to appreciate more the older I got. When I started taking seminary classes in ninth grade, my teacher was impressed by the depth of my scriptural knowledge, something I can mostly chalk up to my dad's tutoring.

-Laughter! My dad has one specific laugh that I just love- it's his laugh for when something so unexpected and so surprising and so delightfully funny happens that he can't help but burst out with a laugh. Also, for a while when I was a teenager, there was an unintentional Sunday dinner tradition that Dad would start telling a joke, but have to re-start it several times before making it all the way through the punchline because he'd be laughing so hard. Usually Tim was sitting next to him and Tim would also start laughing, which would make Dad laugh harder. The rest of us would usually start giggling in sympathy after a while. The jokes were never as funny as watching Dad and Tim laugh.

- Piano music. He doesn't have as much time for it as he used to, but I have wonderful memories of "dancing" around the living room while Dad played the piano when I was a child. He really was quite an accomplished pianist- and still is, although his skills are a little rusty at present. One thing that makes me more nostalgic than just about anything else is hearing Chopin piano pieces.

- A sense of humor. Maybe this should be coupled with laughter. But to finish up, I can't resist sharing how a couple of my brothers have chosen to celebrate Father's day in the past (when, to their credit, they were much, much younger).

One of my brothers wrote my dad a very nice Father's Day card that read,
"Roses are red
"Violets are blue
"some dads are nice
"So are you."

Which can only be topped by another card he received which read,

"Dear dad, even though you're not famous, I still love you."


On another occasion, one of my brothers decided that for a Family Home Evening lesson on Fathers' Day, we should all look up scriptures about fathers. He found a couple in the index and didn't bother to review them before he read them out loud to us. So he was rather surprised when he found himself reading this scriptural gem out loud:

"And because he had fallen from heaven, and had become miserable forever, he ^asought also the misery of all mankind. Wherefore, he said unto Eve, yea, even that old serpent, who is the devil, who is the father of all ^blies . . ." (2 Nephi 2:18)

The moral of the story is that a little preparation goes a long way. Also, to my dad's credit, he laughed harder than the rest of us when the verse was read.

Happy Fathers' Day, Dad.

The first campout

Last weekend was the first campout of the summer! One beautiful thing about living right by the mountains is that decent campgrounds can be reached by driving for less than half an hour. Very good. The participants in this campout were me, Katherine, Kent, Curtis, and Angi. Angi and I felt kind of left out because our names don't start with a "k" sound.

It rained all week but the forecast claimed that it would be dry Friday afternoon to Saturday afternoon. We decided to believe this and headed up the canyon. Katherine packed plenty of food and Curtis did his best to eat as much as possible. He also brought a large knife and we tried to think of good uses for it. At one point we saw a deer and we thought he could catch it and gut it for our dinner. In the end, we settled for hot dogs.

It was an enjoyable evening. I kept waking up during the night and giggling to myself over the memory of the witty conversation that we'd had around the campfire.

However, early Saturday morning we discovered that the weather forecast was WRONG! (I guess I souldn't really be surprised). There was the sound of merry, unrelenting rain upon the tent. Fortunately, both the girls' tent and Kent's tarp did their job well and kept us all dry. Katherine and I went on an early morning walk and almost lost our shoes in the mud. Yum.

We heated up water for cooking eggs and having hot chocolate.


Kent drowned his sorrows in the bottom of a bottle of cherry soda.


I'm not sure what his sorrows were, but he sure did finish off that soda. Then Katherine got a little exuberant with the hot chocolate powder and the result was more chocolate than hot.

Sadly, I do not own water-repellent glasses. And my rain poncho was at home, doing me a lot of good.
We were at the top of the foothills, right by the mountains, and it looked like the rainclouds were going to come right down and eat us. We canceled out planned morning hike and got back to our hot showers early.



Angi wisely stayed in the tent in her sleeping bag until the last possible minute and made a dash for the car. The next camping trip will be longer and drier. I hope.

Did I start something?

Several days ago while I was paying a trip to the greenhouses, I noticed that some of the horticulture people had been working with plants and tossed several perfectly good stems of blooming geraniums into the trash. Not wanting to waste the bright red flowers, I picked them out and took them back to the lab, where I put them in a coplin jar full of water. They withered a few days later, I tossed them out, and kind of forgot about it.

Then on Tuesday, I came up to the lab and discovered a huge red amaryllis sitting in a flask- right by my work station. Today, it is even accompanied by roses in a beaker:



I'm not sure who's behind this and if they are intentionally leaving the flowers by my workbench or not, but I'm sure getting a kick out of it.

Update: The flowers are courtesy of our Bolivian grad student, Amalia. Now I'm really not sure why they're by my workbench instead of hers. She does work with chloroform a lot . . . maybe she was afraid the fumes would be bad for the flowers. I know they're bad for me. :-)

Feeling a little crotchety

I just thought you would all like to know that I finished crocheting my box-stitch blanket and tested it out by sleeping under it the last two nights. It seems to be functional. That is all.

Quote of the Day

My friend Steve has, upon seeing various quotes appear in the tagline of my Gmail account, encouraged me to start coming up with a quote of the day. That's probably not going to happen. But I have found a few good quotes that are probably worth sharing. Here's my first one, which is my current tagline:

"Property and mines of wealth are not to be compared to the worth of knowledge."
-Brigham Young

Good ol' Brother Brigham. I bet he's pleased with the university that bears his name.

Sabbath Musings

I have been reading a book lately that I'm pretty sure is going to be established as one of my long-term favorites, good for reading and good for referencing. It is "The Broken Heart: Applying the Atonement to Life's Experiences" by Bruce C. Hafen, who is a member of the First Quorum of the Seventy in the Church of Jesus Christ of Latter-day Saints. He is one of my favorite church authors because his writing style is so good to read. And, as a verse that I never noticed before in the Book of Mormon, in Jacob 4:12 puts is, "why not speak of the atonement of Christ, and attain to a perfect knowledge of Him, as to attain to the knowledge of a resurrection and the world to come?" Why not, indeed? Why not speak of the most glorious event to take place in the history of God's creation, which is a much larger time frame than I can think in.

I used to have a rather unfortunate view of the atonement, which was essentially that God was going to call me out on my sins and make me repent, which was a word I recoiled from in fear. However, one of the most beautiful things that has taken place in my life is the beginning of an understanding that this is completely not the case. Repenting means changing anything in our natures that is contrary to God's will. It means opening our hearts wide open and letting the Savior in to purify the gold he finds there. This is a scary thing to do. But it is very worthwhile.

With this opening of our hearts to God, many blessings on top of repentance become available. Elder Hafen quotes a scripture from Isaiah in the introduction of his book, found in chapter 61:

The spirit of the Lord is upon me, because he hath anointed me to preach the gospel unto the poor, he hath sent me to heal the brokenhearted, to preach deliverance to the captives, and recovering of sight to the blind, and to set at liberty them that are bruised. To appoint unto them that mourn in Zion, to give unto them beauty for ashes, the oil of joy for mourning, the garments of praise for the spirit of heaviness."

The emphases are Elder Hafen's addition. He is trying to emphasize the fact that the atonement of Jesus Christ does so much more for us than purifying us of our sins, although if that were its only purpose, it would still be a great and significant thing. The atonement can not only cleanse us of the stains of the world, but it can heal us from the pains of the world. It can heal our broken hearts and it can give us peace when we have none and it can fill our hearts with love that spills out until we cannot help but give that love to others.

However, such a precious gift does not come free. It requires work, hard work at that. It is not easy to communicate with God in a world full of distractions. But it can be done. My hero Nephi sums it up well towards the end of his scriptural writings, found in 2 Nephi 31:19-20:

"Behold, ye have not come this far save it were by the word of Christ with unshaken faith in Him, relying wholly on the merits of Him who is mighty to save [ie, the atonement of Christ]. Wherefore, ye must press forward with a steadfastness in Christ, having a perfect brightness of hope and a love of God and of all men. Wherefore, if ye shall press forward, feasting upon the words of Christ, and endure to the end, behold, thus sayeth the Father: Ye shall have eternal life."

What I see when I read this is that Nephi brilliantly gave us a concise game plan for how to use the atonement to make it back to God's presence. We must have unshaken faith in Him and His ability to save us, or change us, through His atonement. We must be steadfast, not easily swayed by every wind and opinion that comes our way. We must have a hope in the power of salvation. We must develop charity, which is the pure love of Christ, or as Nephi puts is, a love of God and of all mankind. We must press forward. No standing still allowed in the Kingdom of God!

And, we must keep doing this, even when we cannot feel God's presence near and we are lonely and tired and depressed. This is called enduring to the end. It is knowing that God is watching over us and helping us even when we cannot tell immediately. It is closely linked to faith. And the prize? Eternal life. That is a prize worth enduring to the end for.

Won't somebody come and play?

When I was a young thing, it was generally understood in my family that it was wisdom to not play Scrabble with Becca or Monopoly with Matt. I believe these games were a sign of things to come, because Becca went on to get a degree in English and Matt majored in economics. There were no games that I was the master of, although I did memorize a children's botanical encyclopedia when I was six and go on to get a degree in plant biology. No one would ever have contests with me to see who knew the most about plants, though. Depressing.

I digress. It is interesting to me that while I have never developed a love for Monopoly (maybe this had to do with the fact that the games took so long and required some sort of monetary prowess which I did not possess. Also, Matt did possess this prowess, and loved playing the game so much that he would give people loans when they ran out of money just so he could keep playing), I did develop a love for Scrabble, and by association, other excellent word games such as Boggle. I can even kind of hold my own against Becca now, and we all actually enjoy playing together, even if I don't win (this might be a good place to insert, before my older siblings can, that I used to be a holy terror to play games with. In fact, for a while, if it looked like I was losing- which was often- then I would be granted points just for not throwing a temper tantrum. Luckily for all, those days have been in the past for well over a decade now).

Upon moving away from home, I discovered that I had a sad shortage of games in my possession. So, seeking to remedy this, Santa kindly gave me my very own Scrabble board and Boggle box for Christmas a year and a half ago. This pleased me greatly! However, I have, since then, come to the alarming realization that not all of the excellent people of my acquaintance enjoy games such as these. So I am on the hunt now for such people. I am looking forward to visiting Becca in a month, because I know she'll play with me. But is there anyone a little closer than California who will engage in a little wordsmith combat with me? I'll even make treats.

The history of nations written in agriculture

Agriculture is such an important part of any culture that ancient cultures built up deities to bless their crops. The Greeks had their goddess Ceres, goddess of grains, and the origin of our word cereal. They also worshiped a lesser-known god named Robigus who protected their crops from devastating diseases, including the prevalent wheat rust.

So many nations and cultures have risen, fallen, and been irrevocably altered by the plants they rely on for survival. With the stratification of our society and the removal of the people from the land, I think that most Americans take that for granted any more. They forget about things like the Irish potato famine, caused by the late blight phytopthora, which destroyed millions of tons of potatoes, eliminating the food supply for millions of people and leading millions to starve to death and millions more to immigrate to America. All because those millions of people lived off of essentially one food- the potato. People also forget, if they ever knew, that the potato is in fact indigenous to South America, and before the Renaissance explorers made their way to the New World, none of the Irish poor had ever seen a potato, much less eaten one. I wonder what they lived off of then?

The potato is not the only plant discovered in the New World that changed the lives of countless people. Tomatoes are also New World natives, along with cocoa beans, squashes and gourds including cucumbers, zucchini, and pumpkins, maize, tobacco, and rubber trees. The conquistadors, being closely connected to the land, saw the value in these new plants and sent them back to their homes where they quickly became ingrained in European life.

However, one plant that played a major role in the lives of the Incas did not get sent to Europe. This was a tall, thin plant with small seeds used like a grain, and it was called quinoa.

Before the arrival of the Europeans, quinoa played a central role in the lives of the people who lived in and around the Andes. It was one of their top staples, along with potatoes, maize, and phaseolus beans. The people boiled it and ate it for breakfast and ground it up and cooked with its flour. They, like the Greeks and Romans, had their own set of deity responsible for keeping their crops alive, and every spring, the Incan Emperor would plant a quinoa seed with a golden spade as an offering to the sun god. Quinoa sacrifices were part of the religion.

The conquistadors, professing God, Gold, and Glory, would have none of that. Quinoa was relegated to the hinterlands where the Conquistadors had no desire to settle. Any attempts they made to take quinoa seed home with them were probably thwarted by the plant's high susceptibility to mildew; if quinoa seeds were placed in the hold of a damp ship, there would be nothing viable left after several weeks on the ocean.

Because of this turn on events, the story of quinoa has been very different from the story of potatoes or tobacco or corn, all the plants that it grew up with. Only recently was quinoa "rediscovered," thriving as the staple crop for the indigenous people of Bolivia, Ecuador, and Peru, high in the Alteplano of the Andes. And it's making a comeback. Because what the Conquistadors didn't know is that quinoa is an amazingly nutritious food. It contains every essential amino acid. It tastes good (if the bitter saponin coating is removed) and is gluten-free. It's every health nut's dream come true, packaged in an attractive, colorful seedhead.

It's also every subsistence farmer's dream come true. For those people who are still connected to the land, who are tied to it and must grow almost all the food their families eat, who can usually only afford to plant a single crop, quinoa is almost too good to be true. And that's why the story of quinoa is the one that's drawn me in- at least for now.