And on the 6th day, he rested.

Or stayed in bed with a pounding headache, the culminating apex of a comprehensive hangover. Although, I doubt God drank an entire bottle of wine when he was done with creation, and the parallel only gets worse. All I’ve done is exercised for 5 days in a row. Swam for 3, ran for 2. Push-ups here, and some crunches there. Again, this is part of my attempt to seriously construct a life worth living. It’s something I’ve been thinking about but putting off. After all, I’m in college. 

Who has time to live a life worth living? There are demands. There are classes and experiments to run and jobs to complete and few volunteering stints and like hey, all of your friends want to go out to the bar tonight but really you just need a night to relax but if you keep putting everyone off eventually you won’t have a social life. This is just a short summary of the past 3.5 years. I always told myself that once I leave college, I’ll be free from a lot of these demands. And I don’t know if that’s true. I think it is–I see myself, living with my husband, in our humble condo or house, with our jobs and our love and ourselves and our time. Happiness through simplicity.

But I can’t guarantee that, and as my therapist noted, I’m so habituated to living a life I don’t find worthy that when I do have the time and the freedom and the simplicity, I might not have the habits to enjoy it. And beyond that, I’m forgoing developing my own sense of resilience. Instead of fetishizing this temporal haven that is always there, in front of me, I need to learn how to always live that life I think is worthy, regardless of circumstance.

The circumstances seem impossible. Finding time to exercise, to peacefully reflect, to have a private relationship with my boyfriend while living in a house of 13 people… it’s a challenge. And this sounds like the typical pre-college pep talk: you’ll have to learn how to organize your time and do everything. But I have succeeded by the eyes of heteronormative and academic standards: I’m about to graduate with straight A’s and high honors, with a fiance to boot!

The data (finally!): in progress, developing, but I think we may soon have enough to start drawing out proposed models and inferring a few hypotheses to test.

I always swim and run at a slower pace than usual. I’m finding meaning in the mundane, in one stroke and then the next and then the next, or finding silence in the monotonous beat of my feet against the pavement. I lose myself in the long black line on the bottom of the pool. I’ve changed my diet (ie: I only had mcdonalds twice this past week?). I’m reminded of Karen Armstrong in her book The Case For God, in which she argues that historically, most spiritual practice was done through ritual. Our idea of religious belief is so grounded in intellectualism that we have supposedly forgotten the attainment of spiritual knowledge through spiritual practices.

In forcing myself to change my life habits when I’ve had an excess amount of time, I understand how taking on different types of rituals and practices can change your outlook and perspective without any serious type of thought or reflection. I think this conclusion is intuitive but it’s not an idea we embrace readily enough. I think we all know that if we passively enter a cultural practice our attitudes, values, and perspectives will start to reflect those cultures.

To conclude, this is something we need to actively engage with more. What is the effect of our rituals? Spending 5+ hours surfing the internet is probably having implicit effects on us, and I think it’s only helpful if, as Socrates suggested, we start seriously observing our lives more deliberately. Is the solution to slim internet time, or to be constructive with it? The answer is probably both–how we do make passive internet surfing become more constructive, either for individual or community growth?

My own prescription for the next week: detail. Write out everything pertaining to what I eat, how I spend my time, and how I feel at set points during the day. I’ve done exploratory experiments in living a worthy life, it’s time to try and place a quantitative net around these attempts to understand them better.

Running With My Shirt On

I went running yesterday.

I run for a few reasons:

1. I have cogent, clear thoughts. I think logically when I run. I think creatively.
2. I feel better when I’m in shape. I like knowing I’m trying to improve my fitness.
3. I like to have an outlet to push myself further than I should. This is totally necessary.
4. It’s cathartic. (related to #3)
5. Minneapolis is gorgeous. The River is gorgeous.

Re #2: I’ve stopped timing and measuring my runs in anyway. I don’t care. Overtime, I do run farther. Generally, I just want to be doing high-activity cardio work for 30-60 minutes. It’s about preventative care. It’s about the free health care I can provide myself.  This isn’t totally selfish–I think doing everything we can to keep our bodies healthy is a moral imperative. If we’re healthy, we are less of a burden on the social safety net. If we’re healthy, we’re less likely to catch and spread infection. If we’re healthy, we can focus our time on the things we do for others.

Re #3 and #4: I don’t really understand myself. I push myself. I have to push myself. I don’t know why. Not everyone is like this. Not everyone chases that adrenaline high and absolute exhaustion just to push myself to run one more mile.

I run with my shirt on.

If you’re running the week before and during Pride, you see a lot of white gay men running. Without shirts on. It doesn’t bother me. I run with my shirt on.

In high school, my tennis coach always explained that if she couldn’t let the girls practice with no shirt on, it was only fair to extend that to the guy’s team. I have never played tennis without a shirt. I’ve actually tried. I can’t. I can’t run without a shirt. If you go watch the music video for Nicki Minaj’s Starships, you’ll hear echos of everyone’s criticism that she oversexualizes everything. Her boobs aren’t natural. Her butt isn’t natural. There are men in that video that are practically naked and ridiculous ripped. No one says anything about them. Leave Nikki alone. Being sexy isn’t a crime if you’re a female.

Go out for a run. Don’t time yourself, except to set a time goal (eg: run for at least 30 minutes). Keep good form, improve your flexibility, and feel your feet fly past each other as you soar down the trail. Run away from the screens and from the construction of modern life. Run to feel alive. Run to solve a problem. Run for your heart. Run for your family and friends.

I am the perfect incubator: An Inspection of the Host-Pathogen Intersection

I am the perfect incubator.

Are you a virus, fungus, bacteria, or single-celled eukaryotic bastard looking to take up residence?

I have hundreds of different cell types–surely one will fit you perfectly! My cells express thousands of proteins, many of which I’m sure you will hijack for your own purposes.

My metabolome has a quick turnover. Fresh ATP at the ready!

Although not poor, I live with many other human beings whom I interact with. I sleep with another human being every night. I work at place where I pass by thousands of people every day.

I am reluctant to buy drugs. Sure, the brute force of natural selection may have already chosen you to be resistant to the drugs I pick.

I maintain an average body temperature of thirty-seven degrees Celsius.

My heartbeat is slow. My blood pH is unique.

I will not die. I will not be the last body you take as a home.

I will beat you, and I will tolerate you. I know my pain well, but my threshold of tolerance is high. You won’t stop my daily routine–you will meet everyone I meet.

But will you love as I love? Will you cry when I cry, and gasp at the stimuli of surprise? Will you overlap my consciousness? When I see my partner and my body is flushed with the hormones that I perceive as joy and love, how will you interact? How will you deal with cortisol, the steroid hormone I produce when I’m stressed? You do stress me out a little, you know.

You are not human. But yet, you may always be a part of my humanity, always a part of our humanity. You, sometimes known as illness, disease, infection–you define our humanity. You bring me sympathy, the consoling words from loved ones, extra tea and chicken soup. You sometimes steal away from us those that mean the most and those that mean the least–that is, those whose lives will perpetuate as a statistic in a shoddy Powerpoint shown in an introductory level public health class. You lead us to innovate, to write, to paint. You create potential, for some of us to be conquered, to be forgotten. You manifest in every symptom, in all people, in all times, in all countries. You are my cousin, derived from an ancestor billions of years ago.

We dream that one day you will no longer share the same temporal and physical geography as us. Eliminated from present space and time. But I believe in you, you hardy little bastard. So, I will tolerate you.

Do we own our own genome?

tl;dr: Zach is further comtemplating whether the way we use language reflects reality.

This week in evolution we are having a discussion on genome scans. There is a small handful of private companies that offer to sequence certain parts of your genome that might give you potentially useful information. These companies claim they can evaluate your risk of developing baldness, diabetes, or blue eyes (hopefully something that has developed by now! they test it anyway!).

One of the prompting questions is this:

Who owns information about your genome? You or the company that gives you the results?

Cue pop culture reference to Michael Crichton novels. 

Really, it’s hard to get into good relevant discussions about most things with lay persons, so hopefully an in-department facilitated discussion will be good. But like, is DNA information something we can even own?

When I consider possession, I think of something you can store and restrict access to. In this way we own land, laptops, stores of food, or in the past, people. But if a company sequences your DNA, they have the information readily available. There’s nothing to stop you sequencing it yourself. Or having someone else sequence your DNA. I’m not sure a DNA sequence (in the form of the data file: ie: ATGCGCGTATTTGA) is really an “ownable” thing.

It’s a law that you can’t patent laws of nature. Yet there is a way to make money off the weather through stock markets. It’s a law that you can’t make money off of people without giving them some of the profit (aka: slavery). Yet people have been making money off DNA sequences and other human byproducts (like HeLa cells) without most people batting an eye. [Curiously, you could argue using HeLa cells isn't at all like slavery and more like owning a cow to produce milk. Some scientists consider HeLa cells a separate species!]

Perhaps, to avoid these ambiguities and confusions, we should just abandon use of any type of language that implies ownership, and instead talk about the ethical uses of information. Surely there are precedents for this. If you steal a small vial of blood from an individual who is HIV resistant, you owe them compensation (and probably jail time). If I donate my blood, and it happens to be HIV resistant, you should be allowed to make as much money off of it as you can. That’s how donation works. You might argue–”I didn’t know my blood could be so valuable. I want compensation!”. But no one would buy that if you accidentally donated an extremely valuable antique to a consignment store.

Conclusion: Can we properly use the verb own in front of any noun? Can I own concepts? Laws of nature? Sets of information? Can I own a word (sounds absurd, but people do own songs).

I Sing The Body Political

[Youtube link refuses to embed! Argh. Foiled.]

I was quoted in the Daily. Oops.

So there’s a lot of noise about this marriage amendment. As there has been. And as there will be, even after the vote is tallied. And my exhaustion will carry on with it.

Honestly, I have an enormous amount of respect for every activist who has been fighting, battle after battle, lawsuit after lawsuit, vote after vote. At the same time, I have to blame them as well for my exhaustion with this issue.

And it is because my body is political. It is not even a choice!

I am gay, and therefore the conservative right deems me damnable.

I am gay, and therefore the liberal left expects me to be an activist. An activist for marriage equality! The rallying banner of the gay world!

I have about as much interest in getting legally married as I do in the stock market. I hope to do it one day, and my life will probably be better off for it, but I know I’ll likely be just fine as I am. I am exhausted of making the marriage argument, and I am exhausted of being expected to parrot it!

I’m sorry for not being sorry. Kids are being harassed in the schools and some of them are dying. And we are forced to spend millions of hours and dollars fighting an amendment that will change very little! If the amendment doesn’t pass, my life goes on as normal. If it does, it makes the future a little bleaker. Kids are still dying.

And no, I won’t buy the nonsense that marriage is a stepping stone, and that bullying will come later. Who the hell decided marriage is a more important stepping stone? Frankly, if we were to better address attitudes towards queer communities, we’d probably lower the numbers of kids being harassed and we’d likely get more votes for marriage equality.

But I mean, I get it. Marriage equality is something you can fight for, something you can write down in the law and see the courts and government dole out your privileges. Tackling the issues of homophobia and transphobia are hard and abstract. And frankly, I’m enormously skeptical that marriage equality will help much. Sure, we may win some over in the fight, but we’re probably digging the trenches between us and them even deeper.

Spending my childhood growing up being incubated with the gross reasonings of why gay people deserve to be a second class of citizens, and then being classed in scientific and critical thinking, has brought me to be even more passionate about wanting to be a teacher and wanting to teach critical thinking to our youth. The freedom that we find when we are rightfully given the tools to search for knowledge is as sweet a drink as we may ever find. For some reason, our schools and our parents have been failing to teach our children that harassment and marginalization of people hardly different from themselves actually drags society down. That these are actually immoral things to do. Perhaps it is because we are too busy telling children to play nice, instead of showing them why.

Voltaire once said “Every man is guilty of all the good he didn’t do.” We need to start reminding people that neglect is just as painful as any other form of abuse. It does no good if you point the finger and say “that’s wrong” while some kid gets his face punched in.

So, when it comes to you, what will you do? Will you do you part and point your finger, vote “no” on the amendment, and move along your way? Or will you go beyond just voting no?

Spread the word. Smile at all. Make a new friend each day.  Step up.

Why I picked biology: the honest truth

I’m working my way through scholarship materials. One essay prompt asks me to lay out why I picked biology as a field of study.

What?

Is there ever a good reason to not study biology? The answer is no, and while I could come up with a gazillion answers to the initial prompt, there obviously has to be some sort of unique history to my path, right? But that’s pretty difficult to tease out, even when it’s the history I lived out.

When I was a senior in high school, I had no idea what I wanted to do. This wasn’t a case of “I don’t see anything that fits me” but rather “Everything fits me.” I had sort of winnowed it down to two areas: music or biology. I played with the idea of civil engineering a lot, and I would have considered English more seriously if it wasn’t an immensely popular major that I perceived as being difficult to making a living off of. I can recall a poem I wrote in my creative writing independent study where I teased out the fight between music and biology, one being the heart of all life, and the other being the heart of all life. What I’m saying is they didn’t occupy discrete areas in my mind.

More/less my decision was made for me. I was rejected by all the schools of music I applied to (one because I choked, and one because I auditioned too late). I could have gone back, and maybe I would have gotten back in. After receiving my rejection letters, I wavered for a month before deciding what to do. But in that month I flourished. A long-term relationship had just ended, my coursework was light (independant studies in Calc 2 and creative writing…band…german…AP English…), and I spent my free time practicing theatre, participating in quiz bowl, and hammering out laps in the pool. I had plenty of time to think and interact meaningfully with the people around me, and it was in that time that I took all of the reasons I loved biology and I synthesized them.

What is the origin of life?

How does life work, on the molecular level? What makes us live? What makes me cry, laugh, think? What are the interchanges of the molecules in my cells? What are the molecules in my cell?

Why does my dog smile?

How do predator/prey relationships evolve (I had studied this using differential equations in calculus, and I was extremely interested in it. Now, not so much. That’s okay)?

How can we fight the myriads of diseases we ecounter?

How is the life of a microbe related to the life of a human being? IE: What is the foundation of biological life?

I did not want to be a doctor. I had no idea what I was going to do with a degree in [biology]. Today, I study biology because of my same thirst for knowledge, but I also do it because I want to make our society a better place. I want to help  people live better lives by enabling them to be more scientifically literate and critically minded. I want to share my awe of life that has made my life so fulfilling with everyone else. And becoming an educator in addition to a scientist seems to be the best way to do that.

Yeah, I was rejected by the music schools, and it’s easy to say that the choice was made for me. But had I been accepted, I might have made the biology choice regardless. In fact, as much as I love and adore music, I partly regret considering denying myself a life of studying the biological sciences. And my need to understand the heart of humanity has been fulfilled.

Independent Projects: Morality, and other readings

I’m in the midst of Sam Harris’ The Moral Landscape, in which he argues that morality is an objective concept that is open to study by science. There are a few ideas which are important:

1.) There is no idyllic view of morality, just like there is no idyllic view of health. That is, medicine nor science can came up with an idea picture of health that applies equally well to everyone. Regardless, we still rely on science to tell us how we can live healthy lives.

2.)A moral truth can be objective but not absolute. It is like in chess, when you have a queen. It’s a good general rule to say “Don’t lose your queen”, and in many cases this is objective fact that it is bad for your strategy, potentially crippling, to lose your queen. Alternatively, there may be instances when losing your queen is the only thing you can do to win.

3.) The difference between answers in practice and answers in principle. If you accept the idea of an objective truth, you acknowledge that there is an answer to a question like “How many are born in a minute” even if science does not have the tools to answer it.

4,) Morality is dependent upon consciousness.

All in all, an intriguing read I expect to finish soon. Honestly, I would not have started Harris unless I had been sparked by questions raised during a reading of a book I’ve read already–Wicked–which raises good questions about intentions, morals, relativism, and the existence and persistence of “good and evil” in the world, and what those two things really are.

I’m also currently picking my way through Darwin’s Origin of Species, a slightly daunting task that is nevertheless rewarding. Crucial is being able to access the Victorian stylings and prose of Darwin, and this requires a higher demand of concentration and involvement from the reader. Certainly a more difficult read by default. Darwin’s style is remarkably logical and well structured for the scientific thinker, as hypotheses are stated bluntly and examined with a microscope.

Lastly, I’ve continued my jaunt through The Rest is Noise, a sort of survey of 20th Century music by the music critic Alex Ross. I do not like rushing through this one, because taking the time to listen to the music he discusses is valuable.

For the future? I’d like to continue Macguire’s Oz series (sort of trashy, but trashy like Knorr Teriyaki Noodles—soooo delicious! The Hunger Game series is second in this list). Thomas Mann’ Magic Mountain. And I want to get back into scifi again, so I’m considering an Asimov staple, or perhaps Bradbury. Of course, this is in absolute ignorance of my already existing to-read list (and this is only what I’ve conspired to actually write down somewhere, I’m sure more await on the periphery of memory):

• Catcher in the Rye
• The Art of Racing in the Rain
• Kite Runner
• Unweaving the Rainbow (a treatise on the relationship between science and art)
• A Madman Dreams of Turing Machines
• Zen and the Art of Motorcycle Maintenance

I think that’s all for now. Remember that winter break is a time of relaxing, but it’s important to dispel restlessness with invigorating ideas. We are close to having only a week and a half left! Prepare wisely for Spring 2012! Enjoy a song from an album I almost had forgotten about!

These are a few of my favorite things!

In the Sound of Music, Julie Andrews sings:

When the dog bites
When the bee stings
When I’m feeling sad
I simply remember my favorite things
And then I don’t feel so bad

And in a time when all students are spending their time buried in books and toppled by final exams and projects, it’s good to take a break and remember some of our favorite things. I have exams mid-week and I’m thoroughly stressed by them. So- here are some of my favorite things!

(Note: This is quote a long post with a lot of media! I’ve put it all below the break!)

 

Animal Diversity: Deuterosomes

I have my last midterm in Animal Diversity Lab on Wednesday (eeee!). It’s basically on all of the deuterosomes well cover with the exception of mammals. The taxonomy we’re covering is listed below.

• Phylum
• Subphylum
• Superclass
• Class
• Echinodermata
• Holothuroidea
• Echinoidea
• Asteroidea
• Ophiuroidea
• Crioidea
• Chordata
• Tunicata
• Cephalochordata
• Vertebrata
• Agnatha
• Cephalaspidomorphi
• Gnathostomata
• Chondrichthyes
• Actinopterygii
• Amphibia
• Reptilia
• Aves

So, if you’re wondering, spelling counts, and yes organizing animal phyla details by the colors of the rainbow does help. 

What’s characteristic about this set of animals is that they are all deuterosomes–that is, the fate of blastopore is to develop into the anus. The second opening develops into your mouth.

The second important point here is that chordates are introduced after the echinoderms. (“after”). Chordates all share the same 5 features at some point in their development:

1. Notochord
2. Pharyngeal gill slits
3. Dorsal, hollow nerve cord
4. Postanal tail
5. Endostyle (thyroid gland)

Yes, tunicates are not only animals, they're chordates!

That’s remarkable because chordates are such a diverse group of animals, ranging from us to lampreys to tunicates. And while adaptations between phyla earlier weren’t too amazing, the adaptations within the classes of Chordata are immensely interesting as we begin to see how species have dealt with extremely differing ecological niches.

For example, the sharks and rays of Chondrichthyes have a cartilaginious skeleton and extremely fusiform body. Their enormous livers help them stay relatively buoyant in the water, and their sensory organs (olfactory, hearing in the lateral line, and electroreceptors in the ampullae of Lorenzini) make them master navigators and predators. Characteristic of vertebrates, they have a closed circulatory system with a chambered heart. The notochord has developed into a vertebral column that encases the dorsal nerve cord, and the organism exhibits bilateral symmetry (a trait that is very ancestral).

Their partners in the sea and lakes, the bony fish of Actinophterygii, have different adaptions. Sharing characteristic vertebrate features, they have an extra fin and gill operculum. The operculum beat water over the gills to maintain constant respiration–sharks must constantly move to do the same thing. Bony fish do not have the same type of liver, and use a swim bladder instead to help maintain underwater buoyancy. Clearly, the most obvious difference is a bone skeleton.

The jump of our ancestors from water to land is best understand in the class Amphibia, including our friends the frog, toad, and axolotl. Amphibians are tetrapod creatures that do not undergo direct development, often having an aquatic larval stage followed by a terrestrial adult stage. They are ectotherms, or cold-blooded, so they have to maintain body heat through certain behavioral mechanisms. Their skin is thin and they have a 3-chambered heart. This is because amphibians breathe through their skins as well as through lungs. If they had a 4-chambered heart, the blood pumping past their skin would have no CO2, a necessary component for the passage of O2 into the blood (as what happens in your lungs!). 3-chambers (in which 1 chamber does not have separation of oxygenated and deoxygenated blood) help maintain a “healthy” CO2 concentration. This allows amphibians to respirate underwater.

The class Reptilia shows adaptations for totally terrestrial life. Whereas amphibians had to lay their eggs in water to prevent desiccation, the tough leathery amniotic eggs of reptiles can be laid in dry areas. Reptiles also have scaley, keratin-laced skin that protects them from water loss. Most reptiles do still have the 3-chambered heart, although the large alligator and crocodile cousins have evolved a 4-chambered heart (an example of convergent evolution with our own heart). The last important adapation was the introduction of a trachea and the ability to create negative pressure in the lungs (like we do with our diaphragm)–amphibians are required to gulp down air!

Aves is our final class of study for this test: the birds. Most birds are fliers, and their bodies show it. Their structure is modified to be extremely aerodynamic with muscles bunched near the pectoral region to help with the beating of wings and a large bone drawing down their belly which acts as a keel. Hollow bones are fortified by a cross-structure and help reduce overall body weight. The scales from Reptilia have been modified into feathers, although the scaley skin remains on the legs. This was likely first done to help maintain internal body temperature, so it’s not a surprise that in combination with their quick metabolism that birds evolved into endotherms. They also contain a 4-chambered heart that allows total separation of pulmonary and systematic circuits. What I found intriguing was the lack of a stomach, replaced by a crop and gizzard instead. Lastly, birds are extremely conservative. They compound their nitrogenous waste into all solids, reducing their overall water weight.

I’m sure you’ve enjoyed this quick study session as much as I have. If I’ve made any mistakes, I apologize–this was a rather quick survey of my notes.

While molecular biology continues to be far more interesting to me, the world of zoology and botany is still academically rigorous and interesting. I’m sure zoology is more interesting to the lay person than the molecular mechanisms of viral lytic infection… But such is life, and certainly ecology has informed molecular biology, as has molecular biology informed ecology. It is an intricate web we weave as we study biology, but arguably the most important. Next: Mammals!

Bonding

Guys,

This is so important.

It’s a phosphodiester bond. This is the glue that holds you together. BASK IN IT.  And never ever forget that word. Phosphodiester.