Don't Shake the Flask

Because you don't know if it'll explode

Month: February, 2011

Microbes for the Lovelorn

The host-centric view of the numerous symbiotic, commensal, and pathogenic bacteria living on and in us is that they’re merely microbial hitchhikers and roommates. They’re small organisms that might make us sick or exchange nutrients with us–but they’re also just that–separate organisms. However, as researchers look closer at the relationship between host and microbe, it turns out that things may not be as straightforward as one might learn in a grade school science class. Instead, the crosstalk between bacterial and eukaryotic cells is a complicated web that influences host immunity and even behavior. In the hologenome theory, we might consider our microbes as just another part of us since the microbe-host interactions ultimately influence our fitness in the environment1. So bacteria may not only be their hosts’ roommates but their most intimate confidants, dictating not only when they get sick or how food is metabolized but also more complex social interactions–like their love lives.

In a fascinating paper by Sharon et al. in PNAS2, several experiments demonstrate that mating preference in the fruit fly, Drosophila melanogaster, is mediated by the fly’s gut microbiota. In the initial experiment, lab flies were divided into two groups. One group was fed with starch and the other was fed with a cornmeal-molasses-yeast (CMY) mixture. Then the flies were given a multiple choice mating test where one male and one female fly from each group were placed in a plastic dish and observed over a one hour period for mating behavior. The researchers observed that even after the second generation, the flies preferred to mate with flies reared with the same food source. Preference persisted up to the 37th generation, which was as far as the researchers had tested.

But why on earth would food source affect mating preferences? The gut microbiota was analyzed by 16S rRNA gene sequencing. Flies fed on CMY had a diverse collection of microbes living in their gut. Flies that consumed starch, however, had a collection of gut microbes in which over a quarter of the microbial population consisted of Lactobacillus plantarum. In the next experiment, the flies were fed antibiotics. This abolished the preference and matings became random. Since the antibiotic killed the microbes in the fly gut, it must mean that the microbes were in some way influencing fly mating behavior. In the subsequent test, the flies that had already been treated with antibiotic were fed Lactobacillus plantarum. And lo and behold, the mating preference reestablished itself. Other bacteria, such as Providencia rettgeri and 41 other species, were also tested, but they had no influence on mating preference. So Lactobacillus might be solely responsible for preference.

While analysis of cuticular hydrocarbon levels in the flies show that Lactobacillus may be influencing fly sex hormones, exactly how the bacteria is modulating hormone levels is still unknown. One possible clue might be gleaned from another process that is regulated by hormones–sleep. Trypanosoma brucei is one sleep-altering parasite that infects humans. During an infection, the immune system is triggered. The immune system is known cross-react with hormones. For example, in the early 1990s, a slew of research showed that the immunomodulatory cytokine IL-1 interacts directly with the sleep hormone serotonin3.

Well, what about humans and their gut microbes? No one has yet looked at the relationship of the bugs in human stomachs and human hormone levels, it is interesting that there is variation of gut microbiota between humans due to diet and lifestyle4,5. And while there is the adage that like attracts like that was proven with the Drosophila experiment, we cannot say whether this is a cause or an effect in humans. Or if this even is a significant contributor to human interactions in the first place.

Gut microbes, however, may not be the only ones playing matchmaker. It has already been known for several decades that bacteria cause body odor6. According to Rachel Herz, a scientist at Brown University:

These bacteria feed on the protein on our skin, and as they digest they release gases reflecting their meal. The specific proteins that populate your underarm are genetically determined and reflect your individual MHC gene profile, which is why each of us has a unique smell.

Herz points out that the stuff on our skin includes the chemicals–“quasi-pheromones” such as androstadienone–secreted by our apocrine sweat glands. As the skin bacteria munch and process these chemicals, the gases given off will make us smell either female or male7.

So will the futuristic versions of the little blue pill or love potion number nine be found in the aisles of your local grocery store? Should people pick up a pint of yogurt instead of querying the neighborhood yenta if they want to find their soul mate? I have no idea. On the surface, this seems a bit silly. What we know today is suggestive yet speculative. Your friendly gut microbes probably care less about your love life than your next meal. But it is not inconceivable to think that the human microbiome might become just another one of those dimensions of compatibility an internet dating site might exploit.

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1. Zilber-Rosenberg, Ilana and Rosenberg, Eugene. “Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution.” FEMS Microbiol Rev. (2008) 32: 723-735. (PubMed)

2. Sharon, Gil et al. “Commensal bacteria play a role in mating preference of Drosophila melanogaster.” PNAS. (2010) 107: 20051-20056. (PubMed)

3. Opp, Mark R and Imeri, Luca. “Sleep as a behavioral model of neuro-immune interactions.” Acta Neurobiol Exp. (1999) 59: 45-53. (PubMed)

4. Ley, Ruth E et al. “Worlds within worlds: evolution of the vertebrate gut microbiota.” Nature Reviews Microbiology. (2008) 6: 776-788. (PubMed)

5. Ley, Ruth E et al. “Evolution of Mammals and Their Gut Microbes.” Science. (2008) 320: 1647-1651. (PubMed)

6. Leyden, James J et al. “The Microbiology of the Human Axilla and Its Relationship to Axillary Odor.” J Invest Derm (1981) 77: 413-416. (PubMed)

7. Herz, Rachel. The Scent of Desire. Harper Perennial: New York, NY. (2007) p 150.

Gaming, Usernames, and Design

I came across this yesterday (There Is No Such Thing As A Girl Gamer) and thought that this could apply to a lot of things in general, not just gaming.

The behavior of some people on the internet, especially under the relative veil of anonymity, was one of the reasons why I picked such an ambiguous username in the first place.  It’s probably idealistic to think that everyone should have the freedom to choose whatever username they wish, but in reality there are words and names that have certain connotations that people just can’t mentally shake off.

With a rather socially neutral username, at least random visitors wouldn’t already have a preconception of me when they glance at my ramblings.  But, I think, that’s the problem right there.  If I even have to be socially and culturally conscious about how to pick a fake name in order not to be discriminated against, we still have a long way to go towards equality.

* * *

I’ve been fiddling off and on for a while about writing an interactive fiction game and for various reasons, it has never gotten off the ground.  Last year, around April, I was tooling around with several ideas and unfortunately didn’t get past the point of figuring out how to implement one particular puzzle which involved tinkering around with time.  In retrospect, I think I was being too ambitious.  I’m a writer, not a coder.

This year, I’ve come up with some new ideas.  Ideas that hopefully won’t make me give up simply because my coding skills equal zilch.  So far I’ve decided on a short story I began back in August which was set in an abandoned sky city that crash landed in a caustic lake.  I’m envisioning that in this game, the city will only be one part of the landscape that the player character will explore.  I have at the moment (on paper), a summary of the plot and a map.  I plan on writing everything in a word processor first before implementing any sort of code.

I love the idea of having the reader actually interact and explore a fictional world rather than reading static text, but at this point, I’d be really happy to even have a shoddy and buggy framework up and running because coding of any sort really is not my thing.  But hey, if I find script writing unnatural yet manage to finish one after many years of trying, this can’t be impossible, right?

An Exasperated View on a Saturday Morning

As I told someone else earlier this week, I was going to use this weekend to run some errands that I had put off the previous weeks.

One of my errands was to reserve space for the Script Frenzy write-ins during April.  Reserving the room at Sister’s Brew was a snap.  It was an entirely different story at One World Cafe where I was informed that they had changed their reservation policies.  I would have been fine if I had to pay ten or twenty bucks to get the room reserved for everyone.  But the policy was that everyone who was going to use the room had to pay for drinks and/or food.  I always end up ordering something when I’m using a coffeehouse’s facilities–whether it’s a drink or an entire meal–because I think it’s only fair to do so.  I’m also willing to pay for something if it will allow my friends, and in this case my fellow writers, to use it.  However, I am extremely uncomfortable reserving a location where everyone, including college students with no money, must pay to get room to write.  So I ended up not reserving anything there at all.

In retrospect, I should have seen the writing on the wall when the manager kept avoiding me when I wanted to ask if I could leave a box there for the Nanowrimo book drive last November.

But writers: have no fear. I will schedule alternate writing meetings at the bagel shop and on campus.

* * *

On an unrelated note, I ordered a hot chocolate at OWC.  The barrista was so excited that she managed to make a perfect heart on the surface of my drink, she took a picture of it.  So now, a picture of my drink is probably circulating on Twitter or Facebook (or both!) somewhere.

I ruined the drink by attempting to put a lid on the cup.  I tried every single size of lid, but none of them fit.

An Irreverent View on a Monday Night

Pre-emptive note to UI undergrads: I know your professors made you come to this event.  They probably even asked to you to write a report about it to prove that you went.  I will tell you now that this blog is indexed by search engines and that your professors know how to use Google.  If you try to copy this, they will know.

The line to the Kibbie Dome for Jesse Jackson’s speech was long.  Extremely long.  And it had started to snow.  It wasn’t terribly cold, but then again, I was wearing a coat and a hat with ear-flaps.  It was probably worse for the poor undergrad in front of me who was wearing just a sweatshirt and the silly anti-affirmative action, pro-“Western civilization” protesters standing around with fliers.  (People took the fliers, but only to mock them.)  The line barely moved at all–it took me about half an hour to even get to the doors because security was busy frisking people (and turning away everyone with backpacks).

But I got there in time.*  The opening remarks was made by a freshman undergrad who was a premed chemistry major and also the first black female soccer player at the university. (Personally, I’m thinking why the hell the university didn’t have a person of color on the women’s soccer team sooner, but then I realize it’s Idaho.)  She was the one who introduced Jackson to the podium.

I will be frank: I didn’t think much of the beginning of Jackson’s speech.  It was only so-so and for a while there, I was wondering what all the fuss was about.  But after a bit, he managed to get going with a peppy rhetorical style.  At the end, he had the audience repeating after him.  I overheard someone saying that they were glad that Jackson’s speech was broad and that it didn’t much dwell on his personal views.  I was personally a little disappointed to not hear him say anything controversial.  It was a rah-rah speech, intended to inspire young people to vote and get involved.

Some points I jotted in my notebook:
-The world is multicultural so we shouldn’t see it through a keyhole.
-The next revolution will be televised.
-Fight for democracy, don’t let convenience lead to tyranny, choose sacrifice over the easy way out.
-A brief history of the important people, like MLK who paved the way for blacks, women, and young people to vote.
-Used the Superbowl as a metaphor for equality: violence with civility because the playing field is even and the rules are clear.
-We’re all free but not equal. (Mentions bailouts and health care. Examples of wealth disparity.)
-Recommends broadening world view by breaking out of cliques.
-Most of us make decisions on whether it’s popular or if it would let us win. But should make decisions on whether it is right.
-Character is beyond culture and color (illustrated by Biblical story of the Good Samaritan).

I also took some notes on the Q&A session (paraphrased):
Q: The spirit of the revolutionary students during the 60s is not the same as today.  How should we change this?
A: Don’t fight yesterday’s battle; protect them.  Students should be academically grounded first.  If students are registered to vote, then they have the power to change things such as making the school more diverse.  With social media, everyone’s a neighbor so we aren’t so isolated from faraway places like Egypt.

Q: Since they were not mentioned in your talk, what do you think about gay rights?
A: Gay rights are included in human rights.  Everyone has the right to live, love and be fulfilled.
(Note: At this point, the audience broke out in the most spirited applause heard the entire night.)

Q: How did you survive the assassination of MLK?
(Note: The question included a rambling monologue about the questioner’s husband who dedicated himself to fight for the rights of disenfranchised people in the south and about a broken justice system.)
A: You cannot stop fate and fate cannot stop faith.  Despite the trauma, we cannot let one bullet kill a whole movement.  We cannot mourn excessively since we still have work to complete.  When we fall down, we get up again.  We lean on Scripture to gain sustenance.  Life is not a straight line.

Q: Many prejudices are learned at a young age from the parents.  As teachers and coaches, how can we overcome them?
A: With education.  Students should leave the university differently than when they arrive.  If you dig yourself into one circle, you cannot grow, thus you need a multicultural environment.  That’s why students who go to schools with only one gender or one culture can’t grow.  Once they get into the real world, they’re traumatized.  You must go back home different.  College should teach you how to cope with diversity.

Q: My child was called a racist name on the bus.  How can we tell others that this is wrong?
(Note: The question was a lot more drawn out than this as the mother–in a very emotional state–recounted the whole sorry incident.)
A: Teach your child to cope with it and to reflect.  He’s going to keep on hearing those names.  The problem is not being called names but internalizing it.  The more he can take a hit without hitting back, the stronger he will become.  Don’t respond in kind.  If you’re an eagle, you don’t crawl with a snake.  You keep on flying.

Q: Thoughts on affirmative action?
A: It’s to offset negative action.  It’s the law (Title IX and Title VII), but we can’t stop there.  It’s for all of us.  It’s not a zero sum game.  Race is a factor, but not the only factor.

At this point, Jackson said his adieus and went to answer questions from the media, which will no doubt already be in the local papers by now.

*I somehow ended up in a row of seats between an older gentleman, who seemed nice enough, and a creepy long-haired dude who kept telling the people behind him that he taught sex education to high school students.  I don’t think I’m a terrible prude, but I swore that if he became more squicky than Cthulhu’s loogie and started drooling on the kid in the next row, I would have grabbed the older gentleman’s cane and done something completely non-Euclidean that would have made him regret leaving his mouth unzipped.

Ten Days of Binge Writing

I signed up for Jannowrimo thinking that I could give it a go by writing an entire novel by hand.  I started out doing this, but then I got lazy for most of the month and didn’t write at all.  (I suppose I could give the excuse that I had been busy in lab, but I’m busy in lab all the time.  Half the time, even on weekends.)  It was at the end of the month that I went into panic mode and decided to scrap writing by hand and just type–especially if I wanted to make that 50,000 word goal by the deadline.

Well, I did make it to 50,000–or rather between 50,600 and 52,600 depending on what word counter you’re looking at–squeaking by at 11:50pm on the 31st.  The writing is, well, a hodgepodge of things suffering mostly from Desperate Writing Syndrome which translates to Really Raw Stuff That Needs Heavy Editing.  At any rate, getting to 50k means that once again I’ve avoided loser status in the world of binge writing.  (This reminds me of a post I read on the Jannowrimo forums of one participant finishing his or her story at 45k even though the stated goal was 50k.  Nearing the end of the month, this participant implored the organizers to lower the goal to 45k–as in this particular competition, participants can set their goal to whatever they wish at the beginning of the month–as their story was finished and they could write no more.  This defeats the whole purpose of the challenge.  It’s the equivalent of a marathon runner telling organizers that he should win the race because he feels he’s finished at 25 miles rather than 26.  If you have five thousand words to go, then just write those damn words–whether it’s an extra scene, a sequel, short story or what-have-you.  You can’t win a challenge like this just because you feel like you’ve crossed the finish line rather than objectively doing so.)

Anyways, this was kind of interesting because for Jannowrimo, I’ve actually been only writing for ten days. Eighty percent of the manuscript (that’s 40,000 words) was written in four days–approaching the equivalent of what I can do during the 3 Day Novel Contest.  However, the number of words I wrote on those four days were not equal.  It broke down to something like this:

January 28 – 2,000 words
January 29 – 8,000 words
January 30 – 20,000 words
January 31 – 10,000 words

I also want to note that even though it seems impressive that I’ve written 20,000 words in one day, I had the whole day (minus the brief time I spent in lab) to do it because it was a Sunday.  By contrast, on the last day–a Monday when I had to go to work until at least 5:00pm–I only had six hours left to write 10,000 words.  Basically, I started about 6:00pm (when I got home and wolfed down a sandwich) and just wrote continuously, stopping only for bathroom breaks.  At one point, I was probably averaging about two thousand words an hour.

So, that was pretty crazy. In fact by the end of January I had written over 300,000 words in that seven month period (over a quarter of a million from the last half of 2010).  It’s probably been the most productive I’ve ever been.  For the curious, here’s where all the words came from:

July 2010 (Julnowrimo): 70,000
August 2010 (Augnowrimo): 51,000
September 2010 (3 Day Novel Contest): 34,000
September 2010 (Other short stories): 5,000
October 2010 (Other short stories): 5,000
November 2010 (Nanowrimo): 90,000
December 2010 (Finishing Nanowrimo): 18,000
January 2011 (Jannowrimo): 50,000
Total: 323,000

And while I will definitely be taking it easy (fiction writing-wise anyways) during February, it doesn’t mean that I’m abandoning it altogether.  There will still be short stories to write and edit and submit.  There will be a bit of brainstorming for April’s Script Frenzy, hopefully.  And I might even spare some thought to that interactive fiction project that I’ve been dabbling in occasionally.