Archive for the ‘Lesson’ Category

h1

Biology of 4’33”

August 11, 2012

Sorry for the lack of posts lately. I have been away for a yeast conference and have been playing catch up ever since. The conference went well. I got a lot of really good advice and got to meet a ton of very famous scientists in my field, which was very exciting for me.

The meeting was incredibly busy and tiring though, with sessions and talks going from 9am to like 11pm. I did get a chance to skip out for a few hours, explore the city, (Princeton, NJ) and do a little shopping. I found a pretty cool book that just came out called Where the Heart Beats, by Kay Larson. The book is sort of a mix between a biography about the American composer John Cage and a history of Zen Buddhism in the United States. John Cage, though his music is somewhat popular among certain niche groups, is mostly famous for being a music philosopher of sorts. He wrote a lot of incredibly experimental pieces that played with randomness, formally called chance music. For example, he wrote many pieces for a prepared piano, where the piano had been messed with by placing objects inside it, thus creating some very strange noises. The book has received fairly positive reviews, with the main criticism being that the writer spends most of her time discussing Zen and hypothesizing what Cage would have thought, and not enough time on his music or his later life.

Regardless, the book so far has been a very interesting read and has taught me a lot about Zen Buddhism. I did not know before how important Zen was to John Cage. John Cage’s most famous piece, 4’33” is a piece of complete silence. The orchestra, pianist, etc. enters the stage, sits in silence for 4 minutes and 33 seconds, and then bows and exits. Formally, the piece is divided into 3 continuous movements, but the average audience member would not realize.

The purpose of the piece is to reveal the sounds that are always around us. The sounds of people fidgeting, someone coughing, a door opening in the distance all become incredibly apparent when you sit in silence. Cage wrote this piece wanting us to realize that we are constantly surrounded by music, and that everyday noises are a piece by themselves.

But because I was at a biology conference, I started to really think about what this piece means to me, as someone who is not necessarily as in tune to my spiritual, Zen, side. While all the talks I was attending were about genetics and these incredibly high-throughput approaches to answer questions, I realized that this piece forces us to think about the noise in our experiments. In high-throughput approaches to science, we basically want to test everything we possibly can, or in other words throw a ton of money and resources to test every possible gene or protein in every possible way. What we get out of that is a ton of data that we then have to sort through. But what ultimately gets published as a result of all that data mining, are just the most interesting “hits” or things that passed a certain statistical test above the background noise (or all the seemingly unimportant stuff).

4’33” is not just about listening to silence and the random noises that occur around us all the time. It is about realizing that our entire lives are focused on the signal-to-noise ratio; we want the noise to be so low that the signal is obvious, clear, and easy. We listen to music on noise-canceling headphones to ensure we hear just what we want to hear and nothing else. We shop so that we make sure we see everything available to us, so that we know the choice thing we want to buy was the best. As scientists, we want very clear data that absolutely no one could argue with.

I think John Cage wants us to realize that there is something beautiful about the noise. When we listen to music, it is ultimately impossible to completely remove the noise and hear just the orchestra, the singer etc. Interestingly, I think many people do appreciate the importance of the noise. Obviously CD’s and MP3’s will provide the purest sound, yet old school records and record players are still sold today. That static that comes out of the record player is just as much part of the music.

As scientists, we need to accept the noise in our data and realize that it might be meaningful. We so often ignore the noise, only focusing on the hits because they are so clearly going to give us a reliable result. But who knows what we are missing in the noise?

Advertisements
h1

Networks

September 14, 2009

Sorry for the lack of updates. It’s a busy time.

But I’m going to post this pretty awesome article theorizing how social networks play a role in our health and happiness. The idea of networks is something I’ve always wanted to study more (the sociologist in me). How one person can affect their friends and strangers, how the type-A personality can start a revolution, how ideas and open-mindedness can lead to progressive change, etc.

The statistical work they do is a little on the sketchy side, and the source of data, though large, needs to be a little more comprehensive. But all in all, a good, long read.


Here’s the article

h1

Lateral Meme Transfer

September 6, 2009

So the first paper I had to read in my Cell Bio course was a paper by Carl Woese at the University of Illinois from 1998 called “The universal ancestor.” LUCA, or Last Universal Common Ancestor by many scientist, is our sort of Adam and Eve: some simple cell from which environmental factors and genetic mutations led to the vast array of organisms we see and observe today, including ourselves. His theory, in short, is that LUCA could not have been one species as we know it today, having all of the essential little biological processes we see in our cells or even simpler organisms like bacteria. Instead he proposes that LUCA was instead a community of “progenotes” or extremely simple cells that lack large RNA sequences with each cell providing a different crucial aspect to life. As the community of cells survived, they had to give and share with each other, proving that the cells were not self sufficient as we would see later.

In the paper he says that the method of evolution for LUCA was different than the method we see today. Today we evolve through genetic inheritance. Family trees. Mom and Dad are different from each other, they have a kid, and if that kid got good aspect of mom and good aspect of dad, he will survive to adulthood and produce a bunch of children who hopefully will also have those same good aspects. Aspects in this case being genes that lead to a stronger ability to survive. But in the chaotic … cluster fuck … of the progenotes, everything evolved differently. Calling it lateral gene transfer, he proposes that the cells of LUCA easily shared genetic information. If things worked well the genetic information could move around and be taken by other cells and if things failed, the information would be quickly lost as those cells died. So evolution moved extremely fast with direct genetic movement from cell to cell instead of what we have today that requires slow generational movement.

An interesting aspect of his paper is his discussion on translation. Translation is how genetic information, like RNA and DNA, become proteins, proteins being the workers of the cell. He says the poor early ribosomes, ribosomes being the RNA machinery that does translation, were extremely inefficient. This means that mutation rates were high, and only small proteins could be made from equally small genomes. And with eventual efficient ribosomes being made that had much better accuracy, traditional vertical, family tree inheritance could occur. Because with better ribosomes meant less mutation and larger proteins which could not be genetically transferred laterally. This all just reminded me of HIV. HIV relies on a poorly functioning reverse transcriptase to be able to adapt to anything. But this is a side note and I’ll get back on topic…

While this theory of his is based on supposition, although his reasoning is extremely well thought out and very believable, the idea of lateral inheritance is an important one. I’ve been thinking about religion a lot lately. Being around the nonbelievers (aka, the biologists) have really got me thinking. Biologists tend to, more than any other science, reject religion. This is the result of evolution being a major aspect of our career. “Nothing in biology makes sense except in the light of evolution” a famous quote by Theodosius Dobzhansky. We stake our experiments on evolution. I’m currently working on a project in yeast that looks at a system in yeast that is conserved in humans. Without evolution, I’m wasting my time: who cares about yeast. But with evolution, I’m looking at a system so important to life, even a single celled organism has it.

But is rejecting religion a bad thing?

I’m going to make the case, with lateral gene transfer, that it might be. This is coming from a biologist, remember. A godless biologist at that.

Religion is a very important aspect of our development into society. Religion brings our people together and gives us a culture. For I don’t know how long, religion has worked in doing that. Look at marriage. A religious institution, it has for the longest time, brought two people together to care and nurture their children. What is more evolutionarily stronger than this institution? We have a long tradition of courtship that leads to two dissimilar people (opposites attract) getting together and sharing their differing genes. Then we bind them together to ensure that these children survive the difficulties of childhood and become successful, child bearing adults. Marriage is a meme that proved to succeed in raising tons of strong children, so it stuck.

(Skip this is you know about memetics) A meme is a cultural gene. The theory of memetics is relatively new (1970’s Selfish Gene by Richard Dawkins). It states that we pass down genes to our children. But with human thought, we have developed a new self replicating “gene” that strictly relates to culture. He called these meme’s, or the cultural genes that like genes, go through evolution and natural selection. Some memes survive, marriage, and some die, Pogs. And some memes evolve, in this case religion.

So religion is, in my opinion, the most successful meme(s). It has held so many societies together, keeping children alive, and getting us to work together and live longer. It keeps us moral, defining what is good, like helping out your neighbors, and bad, killing your neighbors. It has led to cultural bloom: JS Bach is considered one of the best composers, and his Mass in B minor is considered one of the best works ever written, and it’s church music!

But only recently have we seen a different ideology spread. With mass communication and an acceptance of free thought, we are seeing it possible to be moral, care for children, form a working society without religion. Atheism is spreading, and not resulting in tons of anarchists burning houses down and lynching Christians. So is this the end of religion? Maybe.

But I doubt it. Because as ironic as it is, religion, specifically Christian religion, has child bearing in it’s roots. The Duggars have 19 kids with more on the way. Not because pregnancy is some kinky infatuation, but because God told them children are gifts from up above, so more gifts are better than less. But that’s evolution! The person with the most successful progeny wins! And ironically, the godless people working in media are providing them with money to show godless America a crazy Christian household. Guess what, the godless are giving this Christian family money to be even more successful, both evolutionarily and societally.

But are the atheists producing 19 children? Are we listening to the word of Darwin and crapping out as many children as we can to spread our thinking in the world. And I have a feeling we’re not. Even Richard Dawkins, who many biologists have come to view as the atheistic leader of evolutionary thought, has only one child. That guy should be producing tons of children to someday spread his thought to the world. He preaches a militant atheism. How does he plan to do it without vertical, family tree inheritance of ideas?

He does it by lateral meme transfer. If atheists aren’t having enough kids to pass this ideology down, they need to spread it laterally. Show the rising youth, confused by war and famine in spite of one dollar spicy chicken sandwiches at BK, a scientific view of life. Show them that hoping for a peaceful, paradise heaven is affecting their happiness in the life they are experiencing today. Show them that they too can have a family, a marriage, and a happy, successful life, without god.

Atheism depends on lateral conversion. So many families are ingrained into their religious ways, and with atheist families so small in number, the only way to make is to convert them.

Will it succeed? I don’t know. My advice? Atheists need to instead of talking about a rejection of God and the importance of evolution, give people a sense that they too can question life, questions fate and destiny, and still create a viable, happy family. And that vertical meme inheritance, allowing your numerous children to also freely believe what they want, and listening to the facts, needs to also be prioritized. It’s worked for religious families for thousands of years. We need to utilize every memetic tool at our disposal. Or else we will see atheism and free thought disappear, just like that your super awesome shiny gold pog that just landed facedown.

h1

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.

h1

X-inactivation

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).