My blog is currently hosted at Field of Science. This WordPress blog is just a backup of the main blog. You are welcome to look around over here, but I urge you to please visit me over at FoS.

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Changes.

On the internet, you're always just a click away.

I have not been posting much lately, mainly because I’ve been going through a lot of life changes and major events in a very short span of time. I defended my thesis, started a new job, and I’m in the process of moving into a new home with the person I love. This is a lot of stuff to process in a short time, and all of it has been amazingly stressful and wonderful. It seems like every corner of my life is rebooting and starting anew, which is terrible and exciting, and suddenly I feel very adult, which is foreign to me. I don’t know. I’m dealing with a lot right now.

I’m both sad and relieved to no longer be a graduate student. Sad because I’m going to miss academia, and I’m going to miss belonging to the tribe of graduate students. Relieved because, let’s be honest, it feels so good not to be tethered to my thesis.

I started my job with nervous trepidation. I had no idea what to expect, because I’ve had lots of jobs but this is the first time I’ve had a career. It is amazing. I love my job deeply, and I am so lucky to have found a job that suits my needs and uses my exact skill set so perfectly. Suddenly a lot of things make sense to me now, like the reasons why people spend so much time and money going to college. It is so rewarding to have a job that you actually like doing!

As for the moving, well, let’s just say I’ll be going from a one bedroom apartment to a lovely condo with two floors and a backyard with ivy and apple trees. I get claustrophobic easily, so this is good news. :)

It only seems fitting, what with the scenery changing in the rest of my life, that I turn over a new leaf in blogging as well. As of this post, the blog C6-H12-O6 will be no more. I have enjoyed my time here at Field of Science and would recommend it to any new science blogger looking for a bit of community and exposure, but it is time for me to move on.

I’ve been invited to blog for the new Scientific American blog network, and I accepted their offer. I’m starting a new blog called Crude Matter as of today, so please come join me at my new digs, read my first post, and have a look around the other blogs on the new network!

If you follow my blog on Facebook, you won’t need to change anything. I will update that page with the new blog information very soon. If you follow me via RSS feed, please switch to the new feed (http://blogs.scientificamerican.com/crude-matter/feed/). If you have this blog bookmarked in your blogroll or internet favorites, please update to the new URL (http://blogs.scientificamerican.com/crude-matter/). I look forward to seeing you there!

Image by Flickr user Andrew Huff.

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Making my own history.

When Alberto at Minority Postdoc emailed me to ask if I’d be interested in writing for the Pride edition of the Diversity in Science blog carnival, I initially said yes, that I’d be delighted to write a post. But then I had a great struggle finding topics to write about. Not because I don’t have plenty of experience being a member under the LGBT umbrella, but rather because I can’t think of ways that my bisexuality and my science have intersected or influenced the other. I have known that I wanted to be a scientist since middle school. I have also known (in some way, though maybe not always explicitly) that I was attracted to both of the normative genders* since middle school. Since then, however, it is hard for me to come up with examples where the two paths have crossed in any significant way.

On Twitter, Kevin Bonham posited that this may be a testament to the liberal nature of academia. I’m not entirely sure that that’s true, although I don’t deny that academia is one of the most accepting environments that I’ve ever been fortunate enough to belong to. I have always been “out”, but often people will subconsciously normalize me as being “straight like them” because the subject of my sexuality never has the chance or reason to come up. The people in science that I have had the opportunity to come out to have been overwhelmingly accepting, though.

One of the suggestions for the carnival mentioned talking about mentors. When I was in high school, I knew a woman who was a wonderful mentor to me. Her profession was in the life sciences, and through my interactions with her I fostered my love for zoology. I had always been a science nerd as a kid, but it was the work that I did with her that really solidified my desire to be an animal biologist, even if I didn’t realize it until halfway through college. This woman was absolutely stunning, smart, confident, liberal-minded, and a tad bit geeky. In short, she was everything I wanted to be at 17. I modeled myself after her in certain subconscious ways (I even picked up some of her vices in college), and there was a wonderful familiarity about her that I couldn’t shake. I admit it; I probably had an enormous crush on her. She was married, but she really struck me as the kind of woman who couldn’t have escaped college without having at least one lesbian fling. I think we tend to know our own kind, but she never came out and told me one way or another. My mind may be playing tricks on my memories, who knows, but I consider her my first and only queer science mentor. It almost doesn’t even matter whether she was actually queer or not. Like it says at the end of the movie The Watermelon Woman, sometimes you have to create your own history.

Actually this brings me to a good point, though, because women like me are sometimes hard to pinpoint. They say that gay people are an invisible minority, and I think that as a bisexual woman in a committed relationship with a dude, I might be the invisible-est. Like I said above, we tend to be able to recognize our own kind, but sexuality is such a private matter that it very rarely comes up in conversations with the people we do science with. My graduate school buddies all know I’m bisexual, but none of the faculty do, nor do my students. I can’t help wondering if maybe I was the unwitting queer science mentor to some other bisexual girl that I had in one of my classes. I’d like to think so. I certainly have gotten my share of strangely personal anonymous student evaluations. Who is to say that they were all from dudes?

The only place where I really feel like I have queer science peers is on the internet. A significant portion of the friends I’ve made through science blogging have come out to me as bisexual in private conversations, even ones I would never have guessed (married, babies, etc.). Part of me really wants to ask whether there’s something inherent about science blogging that attracts the queer girl demographic, or if we are just representative of a large silent minority of queer lady scientists that nobody knows about because we keep our shit to ourselves.


* A note on labels: Some people dislike the term “bisexual” because it imposes a false binary on gender, and prefer the term “pansexual” instead as a term that encompasses all gender permutations. I think this is a valid argument, but I still choose to use the term bisexual because my sexuality does fall fairly hard along the normative gender binary. I like feminine girls and masculine dudes, so classic gender roles are what I seek in my relationships. I do not deny the existence or validity of other gender permutations; they just don’t get my rocks off.

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Circumcision and HIV: why I’m not convinced.

Cassandra Willyard has a blog post up at The Last Word On Nothing: Why Circumcision Protects Against HIV. Frankly, I am not convinced. Cassandra cites three studies in three different African countries that test the HIV infection rates of circumcised and uncircumcised men. She writes: “In each study, they enrolled between 2,000 and 5,000 HIV-negative men and circumcised half. Taken together, the studies found that circumcision reduced a man’s risk of contracting HIV by about 60%.” The results are undeniable, but in the comments I cautioned her to avoid extrapolating these results to the relationship between circumcision and HIV in other parts of the world. She responded with “A penis is a penis, no?”

Well, yes. And no. The reason why circumcision is a popular public health initiative to prevent the spread of STDs in African nations is because there are barriers to the use of other, more efficient prophylactics. Condoms are often cited as being from 60-96% effective against the spread of HIV, but condoms are not as easy to obtain in Africa as they are in the USA, for example. In that context, circumcision is an effective way to slow the spread of HIV in African populations. It’s certainly better than nothing, but the important thing to remember here is that public health initiatives are highly context-dependent. Should circumcision be promoted as a way of stopping the spread of HIV in the USA? I don’t think so, because we have easy access to condoms and sexual education services, which are more efficient at reducing the risk of HIV infection than circumcision. After taking condom use into account, there are very diminishing returns on the benefits of being circumcised.

Additionally, there currently isn’t an agreed upon mechanism by which circumcision would provide a physiological barrier to infection with HIV or other STDs. Cassandra does a good job of citing the possible mechanisms, but she also mentions that all of these mechanisms have had mixed results in the literature. I honestly think that there’s a very large behavioral component to the risk reduction seen in these African studies. The men in these studies were all circumcised in adulthood, not as infants, and as I said in the comments at Cassandra’s post: “The act of having the surgery might influence the sexual practices and behaviors of the men in the study. I imagine that if you have surgery done on your penis, it isn’t a stretch to imagine that you’ll start using it differently.” I would really like to see a study that addresses the effects of the frequency of sex, duration of sex, number of partners, types of sex acts, etc. after having the surgery. I’d also like to see a study that compares HIV infection rates in men circumcised in adulthood with those circumcised in infancy.

In the interest of full disclosure, I need to state that I am morally opposed to circumcision. However, I think the question of morality is irrelevant to this conversation, since policy shouldn’t really have anything to do with my morals. My morality isn’t the same as your morality, and that’s fine. I’m also morally opposed to abortions, but anyone who knows me knows I’m very pro-choice. I am pro-choice when it comes to circumcision too, but I am against it being promoted as a prophylactic in places where there are simply much better options. I think in the USA we have this strange aversion to foreskins as “yucky”, which also comes across a little bit in the language Cassandra uses in her post (she refers to foreskins as “weird”). As a society, we engage in normative behavior where circumcised penises are the default and uncircumcised penises are somehow dirtier, “weird”, or unpleasant. I find this very problematic.

As an aside, I should really know better than to engage the circumcision crazies on the internet. One day I will learn. I’m not referring to Cassandra here, but rather the type of people who seek out and comment on blog posts about circumcision. They tend to have a special kind of crazy. Perhaps I am one of those people..?

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Links – June 2, 2011

A few orders of business.

  1. My mitosis painting from artologica arrived this week! It is gorgeous and I can’t wait to frame it and hang it in my new condo.
  2. Add this blog on Facebook if you wanna.
  3. I PASSED MY THESIS DEFENSE!!

I’ll get back to posting soon. Now some links. Some of these are kind of old since I’ve been in the thesis defense cave. Sorry.

Physiology

Semen allergy suspected in rare post-orgasm illness. Some dudes are allergic to their own semen and become ill for weeks after ejaculating. On the plus side, hyposensitization therapy seems to work for some of these dudes.

Human skin cells turned into nerve cells. Epidermal cells from circumcised foreskin are being turned into nerve cells via a reprogramming called transdifferentiation, which is faster than converting adult cells into stem cells and then back into some other type of cell. Unfortunately the success rate is very low.

Anorexic brain responds to food anxiously. Instead of releasing dopamine in pleasure centers like most people, food causes anorexics to activate areas of their brain associated with anxiety. Considering my phobia and my own battle with my relationship with food, I can relate to that.

Blue lights show to give brain a boost! But is it better than coffee? Photoreceptors in the eye that detect blue wavelengths of light boost alertness and concentration. Blue wavelengths are specifically associated with reduced levels of melatonin (which makes you sleepy) in the brain. That’s why I have f.lux installed on all my computers. It automatically turns up the ‘warmth’ of your computer screen after sunset. This way you minimize your exposure to blue light in the evening, causing less inhibition of melatonin release so you can fall asleep easier.

Other Science

Bats use carnivorous pitcher plant as living toilet. It seems that a certain species of bat and pitcher plant have evolved a nice symbiotic relationship. The bat gets a place to roost, and the plant gets fertilizer. Also I just love anything to do with poop, so this was right up my alley. Bats aren’t alone; it seems that some shrews have a similar relationship with another species of pitcher plant.

23andMe DNA Test Review: It’s right for me but is it right for you? This is a good read for anyone considering getting genotyped through 23andMe. It does a bit of explaining about the process and product, and what questions you should think about before deciding to buy. I’m happy with it, personally, but you need to consider what you want to get out of the product.

Mpemba’s baffling discovery: can hot water freeze before cold? A great story about scientific inquiry and battling dogma.

Other Stuff

Calvin and Hobbes Fight Club. Someone did a mash-up of the Fight Club trailer with scenes from the Calvin and Hobbes comic strip. Watch the video!

I’ve gone and done it now: What it’s like without the Muslim headscarf. Interesting read from a woman reconsidering her stance on the hijab.

The National Academies Press makes all PDF books free to download. The title says it all.

The man who wasn’t there. There’s been a lot of buzz lately in my meatspace life about the circumstances surrounding Jim Tressel’s resignation as the Ohio State University football team’s head coach. I’ve been finding it hard to care very much because football isn’t as important or interesting to me as it was once upon a time. However I did like reading this post, which has an interesting take on his legacy.

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Links – May 24, 2011

My thesis defense is in one week (whoa!), so I’m taking a break from blogging to go into hardcore study and preparation mode. I’ll see you back here after June 1st, hopefully with good news!

In the meantime, here are some links to hold you over. Also, I made a Facebook page for my blog the other day on a whim. It occurred to me that there are some blogs I follow through Facebook that aren’t in my RSS reader, so I’d like to have that option available for people who maybe do the same. You can ‘like’ it if you like this blog and like ‘liking’ the things you like.

Physiology

Does sexual intercourse hinder subsequent athletic performance? Many athletes superstitiously abstain from sex the night before a big game, meet, or performance, but is there actual evidence to support this belief? Some say it reduces testosterone and energy the following day, but it seems that there aren’t any studies that confirm this suggestion.

Seven Deadly Sins Sunday: Gluttony. The link is to part 5 of 5, use the links at the top of the post to read the earlier posts. A great discussion of the physiology of gluttony. This is becoming one of my new favorite blogs.

Gut bacteria linked to behavior: That anxiety may be in your gut, not in your head. The gut flora may be influencing brain chemistry and behavior.

Other Biology

A map of charismatic canid genomic variation. All that genetics PCA and structure (a program similar to ADMIXTURE) crap, but applied to dogs!

America’s most poisonous pill. It’s not what you think (although the title is more than a bit misleading). Klonopin, a benzodiazepine, is apparently the second most abused drug in America behind opioids like Oxycontin.

Sex, sleep, and the law: When nocturnal genitals pose a moral problem. If someone forcibly tries to have sex with you while they’re sleepwalking, can they be prosecuted?

Other Stuff

Marketing food to kids with cartoon characters. Kids think that food tastes better when there are cartoon characters on the box, and this is true for foods from cereal to carrot sticks. This can be a good way to get kids to make healthier food choices, but chances are that for every healthy food option endorsed by Shrek or Nemo there are a handful of unhealthy ones endorsed by that lemur from Madagascar.

Forensics: The call of the crime lab. A good report on the state of the occupation. I wanted to be a forensic scientist for a long time, but I don’t like chemistry enough to be very good at it.

Happy guys finish last, says new study on sexual attractiveness. “Women find happy guys significantly less sexually attractive than swaggering or brooding men.” Guilty.

What they are really typing. A few studies attempt to quantify what students are really doing on their laptops during class.

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Doug McDonald’s BioGeographical Ancestry Test

In my quest to explore various aftermarket sources of information on my 23andMe raw data, I emailed my data to Doug McDonald for his BGA testing service. I first found out about his service on the 23++ Chrome extension website, although the email they have listed for McDonald is wrong. I finally got the correct email (mcdonald at scs dot uiuc dot edu) through the 23andMe community forums.

Here’s what he sent back:

Michelle: The program says you are English, 100%. However, on the chromosomes one sees a small <.5% American block that is fairly strong and likely real, but not 100% sure. The other blocks on the chromosomes are likely noise.

Here’s a look at the chromosome painting you get from McDonald (similar to 23andMe’s “ancestry painting”):

Click to enlarge

The red sections are European, the brown sections are no data/not enough data, the two small blue sections are African, the small grey section is Mideastern, and the green section is Amerindian. I would like to know which side the Amerindian segment is on so I can explore this further. My mother’s 23andMe results are due any week now, so I will likely email her data to him as soon as I get my hands on it.

You also get a number of what I think are PCA plots, showing where you map out with respect to his reference groups. He only sent one for me, but he sent multiple for my boyfriend. Here’s mine:

Click to enlarge.

The crosshairs show where I fall, in the middle of the English cluster, close to the French side. I thought I had more of an Irish minority than a French minority, but hey, whatever. I notice he doesn’t have a sample German population, either.

Most of this is not new information to me, but does provide corroborating evidence for the ~1% Amerindian that shows up for me in Razib’s admixture analysis. The results for my boyfriend go along more or less with what came up for him at the Harappa Ancestry Project.

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Anti-clotting factors in vampire bat saliva may save your life.

While I’m on the subject of things that suck blood, I’d like to take a moment to tell you how vampire bat saliva may save your life one day.

Today I happened to see a tweet from the Ohio State University Medical Center’s twitter account that linked to a press release discussing a new plasminogen activator that is currently undergoing clinical trials. The drug, desmoteplase, is modeled after a protein found in vampire bat saliva that prevents clots and platelet aggregation, which keeps the blood flowing while the bat is feeding. Plasminogen activators like desmoteplase are used to break down blood clots that are blocking blood flow to vital organs such as the heart, lungs, or brain.

Image credit: Flickr user gandhiji40

To understand why bats have this protein in their saliva and why it may be medically useful, we first need to understand how clots form. Whenever a blood vessel is damaged, collagen fibers are exposed under the severed lining of the vessel. Platelets, one of the several blood cell types, will begin to stick to the collagen fibers and to one another until the damaged area is covered. This creates a platelet “plug” that stops immediate blood loss. Once the platelet plug is in place, a cascade of clotting factors (a vital one being a chemical called fibrin) will build a clot “seal” over the platelet plug that forms a more permanent barrier to blood loss while the vessel heals.

After the vessel heals and the clot is no longer needed, a chemical called plasminogen is activated and becomes plasmin. Plasmin then breaks down the clot by solubilizing fibrin. This is a safe way to get rid of the clot so that it doesn’t come off in one piece and then lodge itself into a small vessel where it can cut off circulation to parts of the body. However, sometimes clots are not broken down properly and can cut off blood flow to the brain (stroke) or heart (heart attack). When this happens, we need to manually turn plasminogen into plasmin using plasminogen activators, so that plasmin can break down the clot and restore blood flow.

Image credit: Flickr user Robertsphotos1

The plasminogen activators in vampire bat saliva were first described by Dr. Christine Hawkey in a letter to Nature in the 1960s. In addition to plasminogen activators, Hawkey later went on to describe platelet aggregation inhibitors in vampire bat saliva as well. Vampire bats do not suck blood directly as mosquitoes do; instead they puncture the skin with their teeth and lap the blood with their tongues as it seeps through the wound. This strategy requires the inhibition of platelet plugs and clots which would stop the blood from continuing to flow during the bat’s meal.

Desmoteplase, which is derived from the plasminogen activators in vampire bat saliva originally described by Hawkey, seems to have some advantages over currently used plasminogen activators (which are often based on chemicals in humans). Current drugs are only approved for use up to 3 hours after symptom onset, and Dr. Michel Torbey at OSU MC is hopeful that desmoteplase will demonstrate efficacy up to 9 hours after symptom onset, which could drastically reduce the number of deaths. From the press release:

“Prompt medical care within three hours is very important for recovery from a stroke, but attempts to find drugs that extend the treatment window have not been successful,” added Torbey. “If the study findings back up our hopes and expectations, desmoteplase could be a real game changer in our ability to help patients.”

In addition to expanding the treatment window, desmoteplase is more potent and specific than current drugs. One current plasminogen activator is even linked to neurotoxicity in some patients, so there is high demand for newer and better drugs to treat problematic clots. If approved, this drug could reduce the risk of death in stroke patients that live in remote areas and may not be able to make it to the emergency room within the three hour window.


ResearchBlogging.orgHAWKEY, C. (1966) Plasminogen Activator in Saliva of the Vampire Bat Desmodus rotundus. Nature, 211(5047), 434-435. DOI: 10.1038/211434c0

Hawkey, C. (1967). Inhibitor of Platelet Aggregation Present in Saliva of the Vampire Bat Desmodus rotundus British Journal of Haematology, 13 (6), 1014-1020 DOI: 10.1111/j.1365-2141.1967.tb08870.x

Schleuning, W. (2001) Vampire Bat Plasminogen Activator DSPA-Alpha-1 (Desmoteplase): A Thrombolytic Drug Optimized by Natural Selection. Pathophysiology of Haemostasis and Thrombosis, 31(3-6), 118-122. DOI: 10.1159/000048054

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