academia

I know what I’m doing in 4.5 years

You and your committee may be the only people who read your PhD dissertation (well, if you’re lucky) – but you can still enjoy is aesthetically:From Street Anatomy:

A long-time Street Anatomy fan and soon-to-be doctor, Stephen, recently sent in this image of an anatomical heart made up entirely of the words from his dissertation. He put tons of effort into studying a particular cardiac arrhythmia, noted below the heart, and instead of hanging fancy diplomas on the wall, he chose to immortalize his time and efforts into a piece of anatomical art.

Someone please remind me of this awesome idea when I’m about to graduate.

End of semester madness!

What am I up to? I’m writing a “fake” research proposal for one of my classes on doing a genome wide association study and exome sequencing to search for genetic components of homosexuality. I say “fake” because it’s a project for a class, not something I’m actually submitting to the NIH or NSF. Well, I mean, I could theoretically submit it as a grant if it ends up being super awesome and a mind-blowing scientific idea, but at this rate I’m just trying to not embarrass myself when turning it in.

On top of that I’m attempting to finish my actual research from this quarter since our presentations are next week. I’m not nervous about the speaking part – heck, I do that for fun now – but talking about science is a bit harder than making jokes about atheism. So, yeah, again – aiming for not embarrassing myself. Frantically trying to learn R to make my graphics, since my professor nearly had an aneurysm when he saw I was using Excel to make my charts.

Aren’t the end of quarters great?!

I know a lot of you are also students – consider this an open thread to complain about all the work you have to do and to procrastinate doing it. Non-students welcome to whine too.

Why my building has key cards


Now I just need to figure out how to make the doors say “Good morning, Ms. McCreight” instead of “Beep.” Then I’ll really be living in a sci-fi movie.

(Alternate reason why my building has key cards: To keep the undergrads out. I like my reason better.)

EDIT: I originally had pi = 0.6 because my project is currently looking at heterozygosity in humans, which is represented by pi, but I realized the inevitable nerd rage I would invoke when people would think I was too stupid to realize pi (approximately) = 3.14. So x it is.

…I have become too nerdy to make nerdy jokes, gah.

Not that this is shocking, but…

“Money for Science May Be Scarce With a Republican-Lead House.” From the NYTimes:

In the Republican platform, Pledge to America, the party vows to cut discretionary nonmilitary spending to 2008 levels. Under that plan, research and development at nonmilitary agencies — including those that sponsor science and health research — would fall 12.3 percent, to $57.8 billion, from the Mr. Obama’s request of $65.9 billion for fiscal year 2011.

An analysis by the American Association for the Advancement of Science looked at what would happen if all of the agencies were cut to the 2008 amounts. The National Institutes of Health would lose $2.9 billion, or 9 percent, of its research money. The National Science Foundation would lose more than $1 billion, or almost 19 percent, of its budget, and the National Oceanic and Atmospheric Administration would lose $324 million, or 34 percent.

And guess who gets to apply for NSF and NIH fellowships and grants next fall? Yep, me! As if they weren’t hard enough to get already. I wasn’t planning on applying for fellowships this year, but maybe I should while there’s still money left.

Well, at least I’m in a somewhat more secure situation. My program guarantees a stipend for the full five years, so I’ll still be able to pay rent and feed myself. And my department has one of the most well funded research programs in the university, so my research project will still probably have funding, especially since I’ll be working on humans (humans really like to pour money into studying themselves).

But the vast majority of science graduate students aren’t so lucky. Even right now, it’s common for graduate students to depend on outside fellowships for their stipends. And if you’re not working on some sexy topic like human disease or biological warfare agents, those grants are going to become even more competitive.

I’m not so much concerned on missing out on the prestige and small raise that would come with an NSF fellowship. I’m concerned that the United States is likely going to fall even farther behind in science.

But hey, I can always go abroad for my post-doc…

I'm published! …Wait a second

More evidence that you shouldn’t always trust Google Scholar to deliver the best research papers. I decided to look up my name to see if my paper on genetic bottlenecks was searchable even though it’s in a book. That’s the third link listed. The first and fourth aren’t me, just some other poor J McCreight who has had their Google image search ruined forever by boobquake. But to my surprise, the second link is also mine (click image for larger):
…It’s a pdf of a paper I wrote my senior year of high school for AP Composition titled “Creationists in Scientists’ Clothing: Scientific and Legal Reasons Why Science Classes Must Omit Intelligent Design.” It’s pretty damn good considering I was 18 when I wrote it, but I derive endless amusement at how serious it’s being treated. Apparently my English teacher is second author, and the journal is ImageShack.

I mean, come on Google Scholar, how unprofessional. You forgot to mention it was 3rd period! What will happen to my academic reputation if someone thinks I was in 2nd period?!

Scientific illiteracy

Reading scientific papers helps me understand why so many people hate or distrust scientists.

Let me clarify briefly. This is not meant to be me bitching about my graduate school workload. This is not me thinking my PhD was going to be a cake walk. I was prepared to finish undergrad feeling like a genius and walk into grad school feeling average. I was prepared to learn, and learning requires feeling stupid first.

This is me trying to think what science looks like to an outsider.

The last couple of weeks I’ve been doing pretty much nothing but reading scientific papers – that is, peer reviewed research papers published in academic journals. Some of these have been historical, the oldest being from the 1940s, and some have been from the last couple of years. Some have been good, some have been excellent, but the majority have made me want to stab my eyes out with the nearest pipetman. I’ve been reading primary literature for the last three years, but dealing with so much recently has made me realize one thing:

Most scientists are terrible writers.

And when I say terrible writers, I’m not just talking about English skills – though that certainly is a problem. When I had to read some of my classmates’ papers in undergrad, I was often thankful to find a sentence that wasn’t a fragment or a run-on. I don’t have perfect grammar, especially when informally blogging, but I can usually get general concepts across. And don’t even get me started on the organization of some papers. Your methods are where?

But most science writing is simply impenetrable. Everything seems to be lingo and jargon, to the point where they might as well be speaking another language. This problem gets worse with time, since fields are becoming more specialized, not less.

And if that wasn’t bad enough, so many scientific papers are drier than Indiana on a Sunday. You would never guess most papers were authored by the same person who will perk up with excitement when you ask them about their research. Obviously papers are meant to be impartial, but that doesn’t mean they have to be devoid of all liveliness. When a paper does include a rare joke, or even a clever ribbing of another study, readers get excited. We like being reminded that humans wrote these papers, not some computer program (unless simulating papers is what your research is about, then…). I nearly pooped myself when I saw a paper use an exclamation mark once. Needless to say, exclamation marks should not provoke this amount of surprise.

So why is this an issue outside of my own graduate school woes? I hate tooting my own horn, but allow me to prove a point. I have a BS in Genetics and Evolution from a respected university. I have three years of research experience in a laboratory. I have one published paper and at least one more on the way. I won the award for Outstanding Biology Student every year I was at Purdue. It’s safe to say that I am more trained in biology than your average person, yet I still have to spend hours reading a biology paper to grasp even the most basic concepts.

I look back on all the times I asked people if they read the original research before passing judgment on a study. Or all the times I sighed at another bad piece of science reporting. Now I just sympathize. If I’m having such a hard time, how do we expect laypeople to understand science?

I’m but a lowly first year graduate student, so I obviously don’t have all the answers… But I’m also a blogger, so here’s my opinion on two things we can do to improve science communication:

Relax pointless publishing rules. Journals are so focused on word count, formatting, figure size, supplemental material… Are you really communicating in the best way possible when you’re worrying about having to spend hundreds of extra dollars for every page you go over? Or when you sacrifice clarity in a graph because it’s cheaper to get it printed in black in white?

One of my papers recently was rejected, and I cringed at some of the questions reviewers had. We clarified all of those points in the initial draft, but they were eventually cut due to word limit restrictions. This is made all the more ridiculous when you consider that most people access journals electronically now. Is the internet not big enough for that extra pdf page? We obviously want some limits so people don’t get excessively verbose, but this is just silly.

Encourage more scientists to be journalists. And I don’t just mean recruiting science majors after they’ve been taught how to write (though for the love of FSM, someone please do that too). I mean encouraging scientists to blog about what they know, and then utilizing those bloggers who have proved their communication skills. It’s hard enough to understand the primary literature, let alone translate it into something people can understand. We need to exploit that talent we have.

The thing that worries me the most? That this is probably just the first of many disillusionments I’ll have about science over the next couple years.

Exposed scientific dishonesty illustrates why science is so great

That title may sound counter intuitive, but give me a chance to explain.

You may have heard about the bit of academic scandal that’s been happening at Harvard recently. Marc Hauser is a Professor in the Departments of Psychology, Organismic & Evolutionary Biology, and Biological Anthropology. He was the leading researcher on the evolution of morality and moral behavior in primates and humans and an author of a number of books, including Moral Minds and (in progress) Evilicious: Our Evolved Taste for Being Bad.

In a somewhat amusingly ironic twist, he was found guilty of scientific misconduct, including fabrication of data that will result in several papers being retracted.

This is a very serious situation, especially since Marc Hauser was such a big name in his field. His career is effectively over, and now reseachers in the field have to rethink everything they’ve learned from him (and cited from him). It’s even more serious for his students, whose futures are uncertain when their graduate advisor has such a black mark on his record. It’s upsetting to the field of science as a whole, which does rely on a certain level of trust for practical reasons. We peer review to the best of our abilities, but you still have to hope everyone else is being honest like you since it can take time to expose problems.

It’s also a little jarring to me personally. Not only will I have to reexamine what I read in one of his books that I greatly enjoyed, but I almost went to graduate school in one of the departments he teaches in. Academic scandals aren’t the best way to start your graduate career.

But we have to remember this is what makes science so great. Science is not dogmatic. It’s based on peer review and constant criticism. Scientists are still human and make errors, sometimes purposefully and sometimes not, so it’s important to have these checks in place. Hauser was a giant in his field, but even he was not immune to scrutiny. It was his own graduate students who brought these problems to our attention at great personal risk.

Some people are using this as a chance to pooh-pooh the whole field of evolutionary psychology. I’m sure it’s only a matter of time for creationists like Ken Ham to squeal with glee and twist the facts for their own “Never trust science!!!” agenda. But I really don’t think this is quite so tragic. Isn’t it good to know that we still expose bad science, even when we may have political reasons to not? Would we rather have evolutionary psychology trucking on without criticism, or get the fraudulent data out in the open? I’d be more concerned with the field if it was just being swept under the table. While it’s sad such dishonesty occured, I’m happy to know that we can still sniff it out, correct it, and punish those who perpetuate it.

Maybe I’m being overly optimistic (I know, unusual for me). But I think it’s good to use this as an example of why science is the best way of exploring the world around us: Because when our findings are wrong, we’ll admit it.

Bias for male lecturers in Physics

Lately there has been a lot of discussion here and elsewhere about male privilege and sexism. I think one of the reasons this is such a touchy subject is because many of our actions that are inherently sexist are unconscious, so we can get especially defensive when people call us out on them. For example, let’s look at how Physics students react differently to male and female lecturers:

Why aren’t there more women physicists, and in senior positions? One factor may be unconscious biases that could keep women physicists from advancing—and may even prevent women from going into physics in the first place.

Amy Bug, a physicist at Swarthmore University, examined the bias question. Her research team trained four actors—two men, two women—to give a 10-minute physics lecture. Real physics classes watched the lecturers. Then the 126 students were surveyed.

When it came to questions of physics ability—whether the lecturer had a good grasp of the material, and knew how to use the equipment—male lecturers got higher ratings by both male and female students.

But when asked how well the lecturer relates to the students, each gender preferred their own. And while female students gave a slight preference to female lecturers, male students overwhelmingly rated the male lecturers as being superior. The research appears in the journal Physics World.

Bug says the results may be evidence of inherent biases that could hold women back—along with economic inequalities, such as lower wages and smaller start-up grants. Which reduce career acceleration and thus the amount of force available to crack the glass ceiling.

Note that it’s not just male students who have some sort of unconscious biases – the female students do as well. This is why it is so important to become aware of our biases. When someone points out that something you said is sexist (against women or men) or that you’re privileged, it’s not to make you feel guilty or like a bad person – it’s to make you conscious of your actions. Only once we are aware of what we’re doing can we actively try to correct it.

Back to the science aspect – I would like to see this repeated looking at scientific papers in addition to lecturing ability. Often times when names on papers are represented by initials alone, people assume those authors are male. If given the same paper, but one with a male name and one with a female, would students say they are the same quality?

I’m also curious how prevalent this is in other disciplines. Is it a science thing, or does the same trend hold in liberal arts? Would it be less pronounced in a field with a more equal sex ratio like Biology? Something I get to think about before I become a lecturer…

(Hat tip to Rugved)

I have my first scientific publication!

My first scientific paper has been published! “Allelic recharge in populations recovering from bottleneck events” by Joseph D Busch, Jennifer McCreight, and Peter M Waser. It’s included in the new book developed by the Department of Forestry and Natural Resources at Purdue University, Molecular Approaches in Natural Resource Conservation and Management:The book was actually released in June, but somehow I missed it. Just found out today because my professor gave me a copy as a going away present.

I guess I’m officially a scientist now. Woohoo!

Evolution 2010 recap

This was my second year going to Evolution 2010, the join meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN). Last year I went as part of the Undergraduate Diversity program (which funded my way!) and had a blast.

This year was just as good. My talk was on the first day of the conference, which was awesome. I only had to spend that morning fretting, and I got to enjoy the rest of the conference stress-free (unlike most of my labmates). My presentation went alright – Prof said I did a good job, but I think I could have been a little smoother. I was surprised that I still had a good number of people in attendance, even though I was speaking at the same exact time as the end of the USA World Cup match. Yes, annoying vuvuzela sounds filled the conference hall.

As for the talks themselves, I went to a lot of interesting ones. Well, the first day started off a little shaky, but the conference improved once I started going to research talks. One of the bad things about the conference was that there were just so many talks – 12 concurrent sessions to choose from! You never know what talk is going to be good, so I know I missed some great ones just by choosing poorly.

The downside of going as a post-bach (I’m in undergrad/grad student limbo!) is that most of the stuff is still way over my head. Almost all of the talks are given by professors, post-docs, or nearly finished graduate students, so no matter how much of a nerdy brainiac I am, I was still way out of my league. So, sorry, no talk re-caps for you. Though Wired did cover one talk that I thought was super cool (and actually understood!), so check it out: Lizard Camouflage Confuses Males About Gender. Pssssssshhhh, Wired covered that but not my copulatory plug talk?

Some amusing things about the conference:

  • I met Jerry Coyne! I was nervous to approach him since he was one of the most famous people there – not just for his blog (which I love) or his book (which my dad loved), but for kind of being the leading authority on speciation. He was super nice to talk to, so my nerves were unfounded. We talked for a good amount of time, mostly ranting about religious accommodationism and evolution. It surprised my lab, though. Or as my professor said, “Even I’d be nervous to talk to him.”
  • There was a Christian Homeschooling Conference going on at the same time in the convention center. There was much loling by the evolutionary biologists. I think at least four different talks I saw made a joke about this is one way.
  • Speaking of jokes, at least two presentations had penis jokes in them. We are so mature.
  • So many nerdy t-shirts! One day I wore the same exact nerdy shirt as someone else, and we kept running into each other and giving each other shirt-props. Also, one day I was wearing my “You say Tomato, I say Lycopersicon esculentum” shirt and I actually ran into someone who studies tomatoes, who informed me that that was not the current accepted binomial nomenclature for tomatoes. Which I knew, but I just found it amusing that this was one of the few places where that could happen.
  • All of the receptions had free “unlimited” (it said limit 2, but no one checked) beer and wine. However, you had to pay 3 dollars for water or pop. I think the conference understood it’s grad student audience very well.

Some amusing things about goofing off in Portland:

  • I went to my first sushi-go-round. I had never heard of these things (mainly because I’m not a huge fan of sushi). Basically they put different small servings of sushi on a conveyor belt, and you snatch the ones you want to eat as they go by. It was pretty good, and that says a lot coming from me!
  • Voodoo Donuts is fucking amazing. It’s a good thing I’m not living in Portland, or I would surely gain 300 pounds. Seriously, I’m going to have to make a trip from Seattle just to get another Old Dirty Bastard. Chocolate, peanut butter, and oreos on a donut? For less than two dollars? Hell yes. All the donuts I tried were delicious, not to mention that all had hilariously inappropriate name. We took our professor there the second night and tried to convince him to get the Cock and Balls. Thankfully he was amused and didn’t fire us all (yet). Also, I was severely tempted to get a The Magic is In The Hole shirt or panties, but I was too cheap.
  • Right next to Voodoo Donuts was a creepy little hentai movie theater. I had to explain what hentai was to my labmates and professor. A little awkward, but at least I didn’t have to explain the concept of waifus or an Dakimakura pillow. It could have started a frenzy or a riot. Either way, a weird thing I might be thinking about my labmates now is if they are going to be into it or not. Like what if they got home after this and pulled up a site like toonsex.xxx? Probably best not to think about it, what anyone decides to do with this revelation is up to them.

Me: It’s anime porn and you can find it at places like https://www.cartoonporno.xxx/ all over the internet.
Labmate: …Why would you watch that instead of the real thing?
Me: Because you’re not constrained by the bounds of reality.

And then the discussion went to tentacles. I mean, how could you not when discussing hentai? I’m just sad I didn’t think to trick my lab into actually going into the theater before they knew what it was.

  • Omg Powell’s bookstore. It was so huge that I seriously got lost. They had a whole aisle devoted to evolution/genetics and a whole column to atheism. I was so overwhelmed I ended up not buying anything!
  • I met a couple of my blog readers, which is always fun. Hi guys! Oh, and Jaki was awesome enough to give me a graphic adaptation of the Origin of Species, which is awesome and made my lab jealous.

I’m sure I’m forgetting some craziness, but that’s all I can remember right now. It was a lot of fun, and hopefully I can go back to Evolution and Portland in the future.

Religious accommodationism at Evolution 2010

Amongst evolutionary biologists, there are differing opinions on how to communicate science to the public and increase acceptance of evolution. One of these opinions is religious accommodationism, which attracts much ire from more outspoken activists such as PZ Myers and Jerry Coyne. While I happen to agree with them, I do understand not everyone does. There are those who believe science and religion are totally compatible, that theistic evolution is good enough, and that we need to mince our words lest we offend liberal theists who could be on our side.
However, I was surprised to find a whole 2 hour symposium at the Evolution 2010 conference devoted to accommodationism. It was the Communicating Science Symposium, which started with a talk by Robert T. Pennock on Communication Evolution, focusing on audience and message. You all know my love for evolution and communicating it to others, so I was initially very excited for this talk. It definitely had good parts, especially about carefully choosing our wording as to not confuse others (Don’t say you “believe” in evolution, don’t call it “Darwinism,” don’t say you have “faith” in science, etc).

But it quickly went downhill. Much of the talk was about distancing support of evolution with atheistic views – that we need to stress that religion and science is compatible so people in the “middle” can still accept theistic evolution. That people are more willing to accept evolution if they hear it from their pastor. He lauded Francis Collins and the BioLogos foundation for being pro-evolution…even though BioLogos just had a piece trying to reconcile Biblical Adam and Eve with evolution.

That’s why there’s a problem with accommodationism. It’s more about winning numbers for your cause than truly communicating and educating people about evolution. Are people truly supporters of evolution if they’re not accepting it as a natural process? Do people really understand natural selection if they think God is zapping in mutations or had a plan for humans to eventually evolve? Why is it that our tactic involves people preserving their religious beliefs (which are based on faith), but molding science (which is based on facts) to fit their world view? If anything, it should be the other way around. Religion should have to accommodate science.

The reason why people feel compelled to do this is because religion holds a special status in our society where it can’t be criticized, even when it’s blatantly wrong. This really came out in the second part of the symposium, which was by a woman from AAAS (I unfortunately missed her name). She said there’s no use in including creationists or atheists in the discussion because we’re extremists who won’t change our minds.

Yep – we don’t want to potentially alienate theistic allies, but it’s totally okay to ignore those atheist extremists. Why is theism worth accommodation, but secular opinions are not? I commented on this in the Q&A, saying if they’re accommodating religion they should also accommodate secular opinions, but all I received was an awkward “Okay” and the Q&A ended – where every other question got a long reply.

I guess it’s just disappointing seeing such a one sided representation of “communication” at a large conference. Should have spent my morning going to the research based talks.

Here, have some links!

In a couple hours I’ll be on a plane to Portland! I’ve set up some posts to go up during my absence, and I may blog at the conference if I get burnt out on evolution (unlikely, I know). Until then, here are some interesting stories I’ve seen recently to keep you busy.