Archive for August, 2009


Going back to my roots, and composting them!

August 30, 2009

So this is my “last weekend of freedom” as so many have put it. Instead of actively trying to seek companionship from, well, anyone in this city of strangers, I decided to stay home and start a major project.

Creating a compost box.

So my mom made me keep this big plastic container. I kind of just kept it in my kitchen not knowing where to put it. Seeing how it sat there very contentedly, I decided to start my own little compost heap. Now composting indoors requires some extremely careful moves, but having spent a summer doing environmental work in the mother of the green movement, San Francisco, I am now a composting pro.

The basics to composting is that you need to compost the right things. Almost all kitchen scraps are fair game, like fruit peels, vegetable scraps, little bread crumbs, pasta that fell on the floor, anything. But the major exception is no meat or dairy. If you thought rancid milk is bad, think about keeping it in your kitchen (Oh yea, I totally drank some rancid milk today. It was horrible. I will now smell every time I consume).

Keep the goal in mind. You want to compost so that you can have beautiful, rich dirt that’s full of nutrients. So what you put in must be what you want to get out. I don’t mean put a corn husk in and get corn out, but what goes into that box is going to be a part of your future dirt. So if you want a rich, nutrient filled compost, you have to put in vegetable and fruit scraps so that the good chemicals in those are part of your dirt, and not wasted by being thrown in a landfill. But if you also throw in a cereal box, well all those chemicals from the advertising will now be in your compost, and eventually your garden, and then your fresh vegetables. So you might as well just eat the cereal box. But that’s being a bit crazy.

But look at composting as the ultimate life cycle in a microcosm. You have what you are eating. But obviously you don’t eat all of, like no one eats that weird rough skin on the outside of carrots. You could just throw it out and add to the landfill. But why not just keep it. Let it get moldy. Watch as the bacteria and fungi take over and decompose your garbage. They will thrive on the crap you don’t want. But the end result is that their waste is something you can use to make plants thrive. And if the plants we are talking about are going to end up on your plate, and eventually a compost bin, the life cycle goes on and everyone wins.

So here are some composting tips.

1. Anyone can compost.
2. YOU should compost. It’s actually really really good for the environment.
3. All you need is any large tub from like, Wal-Mart or Target. Remember, in an apartment you have to do things on a small scale because you don’t have the advantage of the outside world to take care of things, specifically the smell.
4. To start out create a base of shredded newspaper. Sounds kind of weird after everything I said, but newspaper is fully biodegradable and very easy to degrade because it isn’t bleached paper and probably comes from paper that has been recycled so thus is a little bit weak. Also, the inks are non-toxic. But stick to no colors, just to be safe.
5. Now start composting!
6. Especially good things to compost: Tea bags, coffee grounds, egg shells, fruit peels, leafy greens, lemon and lime rinds (they make the environment a little acidic and also help the smell).
7. A big part of composting is this carbon to nitrogen ratio. Most compost heaps basically don’t have enough nitrogen. The newspaper base is extremely carbon high. Most things dry will be higher in carbon. So if you stick to composting a lot of kitchen scraps, you should be good.
8. No meat or dairy!!!

I encourage you all to compost. It’s quite easy. And kind of exciting. I had a fruit spoil, so I just threw it in! Stupid dragon fruit. Not even very sweet. And it stained my cutting board! Hope you enjoy rotting in my new compost box.


Nature’s Struggle

August 27, 2009

So for the past 2 weeks, I have been… Moving. And watching TV. And moving. And not the fun moving like running around a beautiful park or playing some kind of physical activity. Picking up a box, and moving said box. But after 2 weeks of driving, shopping, unpacking, organizing, one and a half seasons of LOST, cleaning, exploring an unfamiliar city, not getting mugged, and a whole summer of Cheers, Frasier, Conan, Big Brother, and countless other trashy reality shows, I am finally running again. To hopefully stand in place.

I haven’t actually had my first real day yet. I spent this week trying to get settled in and find out what I need to start doing. I chose to make my first lab rotation something completely new. I liked the prof’s background: Histone structure. Big deal prof in the world of biophysics is exactly what I need to get a good grasp on something I’ve literally never studied. And I know about histones: they form a protein octamer that together with the DNA wrapped around it forms the nucleosome and activation and repression all have to do with modifications to the histone that may make the DNA looser or tighter or more or less accessible. But seriously, I have no idea how to crystallize a protein. Or do… that’s actually the only technique I’ve even heard of…

But even luckier for me, the professor told me in my first meeting that I may end up doing a joint rotation with another professor. And guess who, another big wig biophysics guy who probably also knows everything there is to know about this field I know nothing about. So after reading 4 papers from the first professor and now another 4 papers from this professor, I am now utterly confused, have no idea what is going on, and tomorrow I will be learning a technique I heard about for the first time yesterday. Awesome.

But what everyone keeps telling me is that this is all worth it. I am literally learning from the best. And even though more sensible people will advise to make the first rotation a bit easier, maybe in something you have some knowledge and background in, I like that I’m being thrown in head first. I like that these professors aren’t giving much regard to my safety as a student. Because that’s exactly what I need. I don’t want to be given an easy project where I just quickly relearn a routine and repeat over and over and get a handful of results. I want to LEARN! This is my chance in life to see the world. To experience science I may never get a chance to see again. So what if I suck. So what if I have no clue. How I adapt and the techniques I learn will make it all worth it, results or no results, happiness or no happiness.

That seems like an overly dramatic thing to say. The lab is actually kind of fun. People are nice. So I should have fun, but do you get what I’m saying? I need to take this time, this year, to learn about biology. I don’t want the easy way out.

In one of my favorite episodes of LOST, The Moth, Locke teaches Charlie about moths. Moth make silk and wrap themselves in a cocoon in which they develop wings and become winged moths. Locke says that he could help the moth get out of the shell by cutting the cocoon open. But the moth would come out of the shell and quickly die in nature. this is because the struggle the moth goes through to pull itself out of that cocoon makes it strong enough to survive the obstacles of life and nature. “Struggle is natures way of strengthening” says Locke. This year is my cocoon. I need to struggle. I need to feel the challenge. It will only make me stronger.

And I can’t help but bring this all to the perspective of evolution. Because that’s really what evolution is all about. Nature throws obstacles at you. And you must struggle to make it out. The weak don’t succeed. And the tough fight to the end. In the end, the moth that breaks free will produce babies that will break free. Now while I doubt grad school is going to leave me with a thousand biologist babies, I do know that if I am not strong enough to make it out of here, I never would have made it as a biologist anyway. But as I sit here, about ready to go watch Big Brother and then go to a gym that I’ve never been to before where I’ll have to fight an old lady for an elliptical, I know how important it is that I keep running. Because like the Red Queen in Through the Looking Glass, I have to keep running to stand in place.



August 11, 2009

Continuation of the unfinished post Women are Winning
The other advantage the girls have over the boys is the fact that they have two X chromosomes, whereas the boys only have one.

This is a pretty basic principle: if you have two of something, chances are it is better than one. For example, diseases and conditions that lie on the X chromosome have no choice but to create an effect in men (i.e. male pattern baldness) while women require the two copies on both chromosomes. So to break that down again, every gene in our body has two copies, one on each homologous chromosome. Homologous chromosomes are pairs of chromosomes with similar genes and are what we inherit, one from mommy and one from daddy. Except boys get one X chromosome from mommy and one Y chromosome from daddy, thus giving you a pee-pee. Girls on the other hand get an X from mommy and an X from daddy, his only one.

So what that means is, if daddy or mommy have something horrible, like baldness, being passed down in their X chromosomes, girls have a better chance of fighting it, whle boys can only hope to dodge it. If daddy is bald, he has no choice but to pass his baldness gene on to his daughter (recall he only has one X to pass on), but as long as mommy’s head is full of hair and passes her beautiful hair gene on, the one copy of beautiful hair can compensate for the baldness gene (more on this later). But sonny boy may not be so lucky. If daddy has beautiful thick hair, well sucks for him it doesn’t matter because daddy is giving him a Y chromosome instead (but if daddy has beautiful hair, then that means his daughter will also have beautiful thick hair because he must giver her that wonderful X). But if mommy has that baldness gene in one of her X’s, he has a 50% chance of being bald, all dependent on which X he gets from mommy.

So to dispel that rumor for boys: baldness is inherited from the mother, but just because granddad is bald, does not mean you will too, and just because he has gorgeous hair does not mean you may not get it either. But ultimately, the advantage is with the girls: by having two X chromosomes, they must inherit the baldness gene from both dad and mom, making the likelihood a bit lower.

But the story doesn’t just end here, and girls have even more to look forward to. Turns out, they only actually need one X chromosome! In a crazy turn of events, female cells actually turn off one X chromosome by turning it into heterochromatin, in other words, packaging the DNA really really tight so it can’t be read, like stuffing books into a closed box and instead of leaving it on the shelf. This is called X inactivation. Early on in development, each cell turns off one X chromosome, making it pretty much useless while the other X chromosome carries out all other duties, and thus making those genes the ones that are used. And which X chromosome turns off? Well it’s pretty much random! This leads to a mosaic in the female body, some cells have one X in use while a cell right next to it may have the other X. So guess what, because this is random, it would actually be impossible to completely clone a female. While creating an exact clone of anyone is pretty much impossible, what with environmental stimuli playing such an important role in development, but from a genetic profile, cloning women are even more difficult because there’s no way to get the exact X inactivation to be the same.

Where this truly plays a crucial role is in the X inherited disease, fragile X. This disease is the result of a neural gene becoming nonfunctional because of a three base pair sequence in the DNA repeating way to much, like 50+ copies instead of 1. This occurs when the DNA is being copied and the machinery literally slips and copies and replicates the same thing over again. For men, if this is passed down to them from one of their mom’s X chromosomes, they will certainly end up with mental retardation. But if a girl receives one bad copy, there is a 50% chance of mental retardation. This is because if certain important cells get the good gene and good chromosome inactivated, then they might end up with problems, but if the right cells get the bad one to inactivate, no phenotype, in this case mental retardation, can be seen. So because the female brain is a mosaic of inactivated X chromosomes, the chances to fight this disease are increased.

Coming back to this baldness gene, the female body is a mosaic of certain X chromosomes inactivated and certain ones activated. That is why girls that are heterozygous for baldness, or have one good gene and one bald gene, end up having hair. Half the cells on the scalp have the good gene while the other half have the bad. So this is enough functional hair genes to prevent baldness.

(Baldness was just used as an example, but I think female baldness is quite a bit more complicated than this. I don’t really know, and once again, I’m not a doctor…)

But does that mean women are better than men? Genetically they may be slightly more advantageous. But that kind of makes sense though, doesn’t it? Women birth our children. They are the crucial people that ensure we have another generation. Men are important too because they create the other half of the babies genes. But while women may only be able to conceive a limited number of babies, men can have as many as they want, assuming they’re players. So maybe ancient Amazonia of lore had it all right, we only need a society of women to get things done, and then the occasional man for the sake of creating a new generation. (And that guy would be really really freaking lucky).


7 days

August 8, 2009

So I will eventually finish my other blog post… In the mean time I’ve been working very hard to figure what exactly is a Chicago accent. The goal is to have a subtle but present accent so that when I move to the east coast, I will stick out just a little bit to give me a small uniqueness. Unfortunately, I’ve been doing too good of a job learning it, and I got it to stick a little too much…

But it is Saturday night. In seven days I will be starting grad school, driving out to my new apartment, in my new city, in my new school, to meet my new friends (hopefully), while sleeping in my new bed (if I can find one), using my new kitchen knives (they’re Japanese which means they are the best according to my mom), in my new kitchen, wrapped in my new towel, after showering in my new shower, etc. etc. etc. Suffice it to say everything is changing very abruptly for me.

How bittersweet. One day you are sitting at home, bored out of your mind with nothing to do but read, eat, practice that new Chicago style, and worry about what’s to come. And all the worrying does is make you dread the day. And then the day comes. You’ve lost your family, your bed, your stability, and are now trying to create a new balance, a new boredom, but with the benefit of having ultimate control, free from your family’s boundaries. You may be teetering and constantly worrying, but all for the benefit of eventually balancing independently. So naturally, I’m ridiculously excited. That’s why this whole thing is so strange. It sucks to have to move, it sucks to have to start over, but ultimately these changes are ridiculously for the better.

Undergrad was exactly the same, but a microcosm. You think you’re gaining independence, you’re finally moving away, to get to do what you want, learn what you want, in an environment of like minded people. And to a certain extent that is very much true. But undergrad ends. And your like minded friends move away. The learning stops, if you even got to learn something you wanted to amidst all the distros and requirement, and you may get to pursue your true passion, if you’ve even figured that out yet. And if you haven’t guess what, you’re back at home, and your independence is gone again.

But grad school, to a certain extent, is what we were all looking for when we went to undergrad. I’m getting true independence by moving to this new apartment in this new state and getting a new drivers license and insurance policies, all being paid for with the stipend I’m getting through school. School has become the job! I’m learning exactly what I want to learn and my job in the end is the job I want to do for the rest of my life (I think). This is the dream. And the most exciting part: all the people I’ll be meeting in a month’s time are thinking the same thing. They have the same dream, and the same interests, and the same fears, and the same hopes. What better than to worry among friends?

And last night, with everything I have to worry about, like moving, buying everything I need, affording everything I need, and grad school in general, the only thing I could worry about were the people I’m going to be working with for the next ~6 years. Who are these people? But really, the thing is, I’m not worried about meeting them at all. I just want to know now what they are like. Who is ridiculously into research? Who just loves science? Who is bitter about the world? Who absolutely does not believe in god? Who is scared about what’s to come? Who else has no idea if this is the direction he or she needs to go?

Seven days I move. In seven days, God apparently created the universe (I’m not really sure about this, someone told me that). Hopefully in the next seven days I will be able to upturn my life. And hopefully, in seven days, I’ll land on me feet and ready to start running. With a subtle Chicago accent.


Women are Winning

August 4, 2009

Over the past year I have heard news twice that men are genetically inferior to women. While this ensures in my mind that the feminist movement can finally declare to the world that they have in fact, well, won the battle, I don’t really know what to think of it. So just to think out loud, I’ll go through both things I’ve heard about this year, and give a little perspective.

1. Y-Chromosome Disappearing

What this article is theorizing is that because the Y chromosome has shown to have lost many of its genes over the course of evolution, the Y chromosome may end up obsolete. Recall that women have genetically two X chromosomes (more on this later) and men have an X chromosome and a Y chromosome. So let’s break this down.

First of all, the idea of the Y chromosome degenerating is not a new idea whatsoever, which the article states. In fact, it has long been thought that the Y chromosome is an already degenerated X chromosome.

Second, the genes the Y chromosome does carry are important for male development. But this does not mean the Y chromosome is the sole necessary thing for man to happen. Male developmental genes are all over the chromosome, which is part of the reason these researchers are theorizing a possibility of Y chromosome disappearance, because the genes that are on the Y chromosome could also find homes elsewhere in the genome.

Finally, this ABC article actually does not make any sense. It is in no way saying the Y chromosome is disappearing. At most, it is saying it may undergo so many changes that it will just not be the same.

But let’s theorize. What if the Y chromosome were to disappear. Here’s what would need to happen.

1. Evolutionarily, a loss of a chromosome would be energetically beneficial. If the cell must work to divide the all the 46 (times 2) chromosomes, it would in theory be less energy to divide 45 (times 2) chromosomes (this is mitosis, or even cell division, or one cell becoming 2 cells by copying everything inside).
2. So the genes on the Y chromosome have to go somewhere. Through genetic machinery like transposons (a complicated bugger, think ferry rides taking genes from one place to another) and genetic conversion (more common, think two cities that look exactly the same and just getting lost and choosing the wrong one) all the genes (according to this article, all ~80) would have to transfer to another chromosome. Each gene transfer though would have to lead to an evolutionary benefit, because while the gene will still be expressed, the different location would have to result in an advantage. And example would be if a male development gene ended up next to another highly active gene and thus make it easier for that one to turn on (for example, having to buy a cucumber and a t-shirt of a cucumber might require going to Whole Foods and the Gap, but it would be easier if you just go to a Super Wallmart).
3. Once all the genes are gone from the Y, the Y would have to be lost due to unequal cell divisions in the testicles, thus leading to sperm with X, sperm with useless Y, sperm with X and useless Y, and super sperm with no X or Y. And then ultimately, these sperm would have to get the egg, which might be more likely because it would be more advantageous if it has more energy due to a lack of a useless chromosome. And then these super no Y men would have to impregnate a bunch of girls (knocked up back of a car style) and pass this lack of Y to all his sons.
4. And these super no Y men would have to some sort of a sexual selection. Maybe the lack of Y gives them a bigger penis. Maybe the easier cell division will lead to an earlier puberty and thus an earlier age to start fatherhood. Maybe it will lead to faster brain and muscle development and lead to a super smart and ripped abs guy. But the gene would have to be passed on to the next generation.

And while this could happen, each step would take thousands upon millions of generations. Changes of this genetic order must take a long time. And with global population and communication making us get to know everyone, the change will take even longer because we’re not even in inclusive societies anymore. And with the sexual revolution allowing everyone to hook-up, even the failures of the world (read: trekkies), the likelihood of this seems low.

Well this was a long post. I think I’ll just leave the next part of my post for next time.


Summer Before Grad School

August 1, 2009

Welcome to my life!

This is the first day of the August, and rightly so, it is my first blog post. And as a first blog post, I guess I should introduce who I am, and what I hope to accomplish. I am an overly enthusiastic wannabe scientist pursuing graduate school because it is the next logical step in my life. After suffering 4 horrible years in a college major I did not enjoy, in a field I did not enjoy, at a school I … enjoyed … I am now hoping to correct all of my mistakes by going to graduate school in my real passion: biology. While this makes logical sense to most, you have to understand, my former major and career path could have gotten me a fantastic, high paying job of my choosing in a suffering economy (I know this because that’s what all my friends are doing). But instead, I’ve chosen biology.

But I have a few goals with this blog I feel I should share:

1. I want to share with the world the crazy adventures or lack there of that the average graduate student in biology undergoes. It’s a tough career choice only the brave and foolish could decide on. Our story demands to be heard.

2. I want people to see how a biologist (at least, this biologist) views the world. If your career is staked not on learning how the body works and what afflicts it like a person in medicine but rather how the cells in your body work and interact and function and allow you to even have a body of interworking cells, your perspective becomes quite different. Also, people asking me for medical advice gets really freaking old (I seriously, don’t know what that bump is on your butt, in my opinion, it’s cancer).

3. I want to teach you a little biology. Biology education has long been considered the “easy” science among scientists and the “memorization” subject among high school students. Somewhere along the way we considered having kids memorize a bunch of bone names and stages in the cell cycle as teaching science. But what this lacks is the magic that is biology. How we come into existence is much more interesting than memorizing a bunch of facts. We need to instill in our children a fascination for biology. Current education does not do that. Biology is not the “easy” science; just ask any sixth year Ph.D. student, if you know one. It is a lot of hard work, and the work people are doing is extremely fascinating; we just need to tell the stories they discover in a better way.

So that’s why I am here. This is the summer before I start. In 2 weeks I will be moving into my new apartment, to begin the craziest adventure of my life. As I work long hours of the day with my right hand pipetteing clear fluids into tiny tubes hoping to god, or shall I say Darwin (no that’s horribly cheeky), that I have some small amount of DNA or protein, and my left hand holding an insane number of journals to read and study, all while sipping from a feed back half cooked ramen noodles just for sustenance and not flavour because my taste buds have de-differentiated back into stem cells on my tongue to be both mean and ironic, I hope I paint you a picture of what it means to be in…