Field of Science

Girlybits 101, now with fewer scary parts!

I was deeply considering a blog hiatus, dear readers, but sometimes you get hit with sledgehammers, and the only thing you can do to make sense of it all is to blog about it.

To make a long story short, Cat Marnell, the "Health" and Beauty expert at XO Jane (a website created by Jane Pratt, of Jane and Sassy fame), wrote a blog post or column or whatever about how New York is out of Plan B and this is very distressing to her because she doesn't believe in birth control and condoms or... something1. It is full of inaccuracies and misconceptions about hormonal birth control, and I am truly disgusted that a woman claiming to be a HEALTH (and beauty) columnist is spreading such filth without checking any of her facts. But I digress. I'm not here to lay the smack down because that's already been done (and better than I could do) by Skepchick and Scicurious (edit: and Kate).

No, what has my feathers ruffled is the part where poor Cat got so flustered by her own cycle that she dissolved into a fit of capslocked hysteria.

It makes me sad that (1) a HEALTH (and beauty) columnist refuses to discuss the actual health involved in the topic she's writing about and (2) this "OH GOD OUR BODIES ARE WEIRD" attitude isn't at all uncommon among girls of all ages. It sorta makes me wonder how much of her own basic physiology Cat actually understands. I think I can help out with that.

This post is a quick and simple Girlybits 101, using very small words and no gross or scary diagrams so that the eternally squeamish and uneducated like Cat Marnell can know a little bit more about their bodies without sending themselves into a hormonal frenzy. I know science is hard, dear, but that doesn't mean you shouldn't take the time to learn it, especially if part of your job description is to talk to women about their HEALTH (and beauty). However, I have to add a caveat. It is very likely that what I'm about to describe doesn't exactly fit your experience! The way women experience their cycles is very heavily influenced by their diet, their activity level, their relative amount of stress, their environment, their age, their reproductive status, how much muscle they have, how much fat they have, what types of activities they perform, where they live, etc. etc. etc. In short, a major theme of female reproductive physiology is that nothing is ever the same, not between women and not even within the same woman over time. My blogpal Kate even writes a whole blog on this topic, which I recommend the more intrepid and less-squeamish of you check out immediately for more information. Kate is a much greater expert on all things ladybits than I am, but I know at least enough to give you this quick non-scary overview.

And now, I present to you this Totally Easy And Not At All Gross Explanation of what happens with your girlybits each month, and how birth control and Plan B tie into the equation.

(1)    You have ovaries, which are a bit like testicles but on the inside. You probably know that ovaries make eggs, but they also make and release endocrines (more commonly known as hormones), which you can think of as messengers. Like letters in the mail. Or text messages, or whatever.

(2)    Every month, one of your eggs begins to mature. Your egg has a comfy little home inside the ovary that provides it all the things a growing egg needs. However, the ovary knows that one day the egg will have to leave the ovary and venture out into the fallopian tubes, where it might possibly meet a charming young sperm and settle down. The ovary wants to make sure that life is easy for the egg when it leaves, so the ovary makes estrogen (an endocrine).

(3)    Estrogen travels through the blood and goes all sorts of places doing all sorts of things. One of these jobs is to build a future home for the egg in your uterus.

(4)    After 14 days or so, the ovary has done all it can do to nurture the egg. Now the egg has to leave the nest and strike out solo. However, this story has a twist. If the egg doesn't meet a handsome sperm and fall in love within about three days, it will DIE!!! (No pressure.)

(5)    After the egg has left the ovary to go look for Mr. Right, the ovary continues to make estrogen and also progesterone, which is another endocrine that has a similar job to assist in building the egg's dream home.

(6)    At this point, one of two things can happen. The egg can meet Mr. Dreamy Sperm at the Fallopian Club, fuse with him, and move into her Uterine Dream Home, or she will die forever alone.

(7)    If the egg dies, the ovary eventually stops releasing estrogen and progesterone (it takes a few days because, uhh, the ovary doesn't have e-mail so it has to wait to get the news of the death through the mail), and a wrecking crew comes by and demolishes the dream home. If the egg fused with Mr. Spermy and becomes a zygote, she starts secreting her own endocrines to communicate with the ovary, telling the ovary what a nice sperm she met and that they're very happy in their new home. The ovary continues to release estrogen and progesterone so that they have a pleasant stay for 9 months, after which a baby magically appears.

Most forms of hormonal birth control interrupt this cycle so that step 4 never happens. The egg never leaves the ovary, so it never has to choose between marriage or death. Plan B can do the same thing if taken before the egg moves out. If the egg has already moved out, Plan B stops the egg and sperm (collectively called a zygote after they fuse) from moving into the dream home. Unfortunately, Plan B can't do anything if the egg and sperm have already moved in.

There, that wasn't so bad, was it? Hopefully some of you are even feeling brave enough to read the more technical version, which I promise is still very easy to understand (however it may include "scary" words like UTERINE LINING and IMPLANTATION and CORPUS LUTEUM, so, you know, beware or whatever).

(1)    You have ovaries. Ovaries are your gonads, or the sex organs that produce gametes, also known as eggs and sperm. Since you're a girl, you're makin' eggs.

(2)    The start of your menstrual cycle is the first day of your period. During and after your period, one of your eggs begins to mature inside one of your ovaries. (Contrary to what some people think, ovaries are not like testes in that they are constantly making eggs. Your ovaries are more like fancy storage compartments than anything else. You already have all the eggs you will ever have when you are born. The ovaries store these immature eggs until puberty, after which one egg matures and is released each monthly cycle.) The egg itself is inside a sphere of special protective cells called follicular cells, referred to collectively as the follicle.

(3)    While the egg is maturing, the follicular cells release estrogen into the bloodstream, which increases vascularization (i.e., it makes more blood vessels) in the uterine wall. More blood vessels means more nutrients for the uterine lining, which may be needed later if you become pregnant.

(4)    After 14 days or so, the egg is now mature and is released through the wall of the follicle and ovary into the fallopian tubes. This is called ovulation and happens because of a drastic spike in a different endocrine made by the brain called lutenizing hormone. The egg will stay alive for about 3 days, during which time it slowly migrates towards the uterus.

(5)    The follicle from which the egg was released begins to die. It is now called the corpus luteum, and it releases progesterone in addition to estrogen. Progesterone continues to build up the soft tissue of the uterine lining.

(6)    If sperm is present in the reproductive tract and fuses with the egg, it becomes a zygote and implants into the wall of the uterus. If sperm is not present, the egg dies.

(7)    If the zygote implants, it releases another endocrine called human chorionic gonadotropin, which communicates with the corpus luteum back in the ovary and indicates a successful implantation. The corpus luteum stays alive for the duration of the pregnancy and continues to produce helpful endocrines. If the egg dies, the corpus luteum also eventually dies and stops releasing estrogen and progesterone. Eventually, your body realizes that estrogen and progesterone levels have dropped off, and this triggers the start of your period. The uterine lining is shed, and a new egg begins to mature. Go back to step (1) and repeat.

Most forms of birth control contain synthetic estrogen and progesterone or just progesterone. By supplementing your body with these endocrines, you (ideally) stop ovulation from occurring. Plan B has a very very large dose of synthetic progesterone and can do one of several things. It can delay or stop ovulation all together, similar to regular oral birth control, but it can also stop a zygote from implanting by irritating the uterine lining (though this mechanism is under debate; see comment #2 over at SciAm). If the zygote has already implanted into the uterine wall, it has no effect.

I used to teach several hundred college sophomores a slightly more technical version of this every quarter.2 If they can understand it, by golly, so can YOU, Cat Marnell! If you have any questions after reading all of that, feel free to give me a call. I would never turn down the opportunity to teach someone about their bodies, as long as they're willing to stop holding their hands over their ears and yelling "LALALALALAGIRLYPARTS EWWW GROSSS P.S. SCIENCE IS TOTALLY HARD, YO" long enough to actually learn something.

1 I am not judging, by the way. I don't like condoms or hormonal birth control either. However I do feel the need to qualify that I am not on hormonal birth control because I have health problems that preclude me from being able to take it, not because I think they'll make me fat. (They won't.)

2 Without fail, every quarter I would have a male student come up to me after a review session or during office hours and tell me in private that he was very glad he took our class because he had so many questions about female cycles that he was just too darn afraid or embarrassed to ask anyone about. It was adorable and definitely made me feel like I had done something good for the world.

Originally posted at Scientific American on October 15, 2011.

Video: Bees at the Wilds

Check out this very cool video about Karen Goodell's research on plant/pollinator interactons, specifically the bee population in an Ohio conservation center on reclaimed strip-mine land. Dr. Goodell is a professor at my old graduate school department at OSU. You can read more about her research in the campus faculty/staff newspaper.

From the feature on OSU's website:
Karen Goodell has a fact that might surprise you: "About 70 percent of flowering plants, including one in three bites of food we eat, require pollination by a bee."

Goodell, a professor in the Department of Evolution, Ecology, and Organismal Biology at Ohio State's Newark campus, is interested in bee populations. At the Wilds--a southern Ohio conservation center located on reclaimed strip mine land--she is studying the relationship between bee communities and prairie habitats.

"Bees are really the organisms that are moving genes around for plants," she says. "Pollinators are absolutely essential for agricultural production. We need to understand what makes their populations thrive."

Goodell’s two projects use 72 different locations dispersed around the Wilds; Ohio State students help her collect data.

"Being a freshman and getting an internship is amazing," says Stephany Chicaiza, who spent the summer after her first year at Ohio State working with Goodell. "I think it puts me at a different level."

Originally posted at Scientific American on September 29, 2011.

Better living through pee-sniffing, or What can urine tell us? Volume 2.

Previously, I told you about how rodents can avoid predators by detecting specific metabolites in carnivore urine, but today I'd like to tell you about some new research being done on human urine in an effort to diagnose certain diseases.

Last week I introduced the topic of metabolites, which are the by-products of the breakdown of things your body consumes, like food, drugs, and vitamins. These by-products are waste materials and usually leave the body via the urine or feces. The metabolites that are present in your urine depend on a lot of factors: not just what comes into your body but also what's happening inside your body. If you are currently hosting a pathogen, the metabolites present in your urine will likely change. This can be directly due to the pathogen itself producing the metabolites (hey, a bacterium has to eat and make waste too) or indirectly by the pathogen influencing metabolic activity (i.e., energy production pathways) in the cells of the infected tissues.

As it turns out, it may be possible to isolate specific urinary metabolite profiles common to people infected with certain pathogens. This could potentially be as simple as scanning the metabolites present in someone's urine and saying, "Okay, you have elevated levels of A and B and lower levels of C and D in your urine, so we have strong evidence that you're hosting pathogen Y." A research group at the International Center for Genetic Engineering and Biotechnology in New Delhi recently approached the question as to whether or not tuberculosis (TB), a disease caused by the bacterium Mycobacterium tuberculosis, can be detected in such a manner by identifying the volatile1 organic compounds present in the urine of healthy and TB-infected individuals.

After screening the urine of healthy and infected individuals with mass spectrometry2, the researchers came up with a few compounds that stood out as being different between the two groups. Two compounds (isopropyl acetate and o-xylene) increased at least two-fold in people infected with TB, whereas three other compounds (cymol, 2,6-dimethystyrene, and 3-pentanol) decreased by about half. To determine the predictive power of these results, the researchers generated a new pool of healthy and infected individuals, and they were able to accurately determine which individuals were healthy and which were TB-infected on the basis of these five metabolites.

It was beyond the scope of this study to determine the physiological origin of these five metabolites, but some of them are related to glycolysis and lipid metabolism, which are two different methods of providing cells with energy via the breakdown of carbohydrates or fat, respectively. It is also unknown if they are originating from the infected body tissues or directly from the tuberculosis bacteria. Clearly more research is needed on the physiology of these metabolites, but for now it seems that they are good potential biomarkers for diagnosing tuberculosis cases through urinary analysis.

But why bother trying to diagnose with urine at all? Traditional culture tests for TB involve taking a sputum (that's the mucus you cough up) sample and seeing if M. tuberculosis bacteria grow from it, but this procedure can take weeks. There's also the common skin prick test, which involves injecting a small amount of bacterial protein under the skin (there is no risk of infection because the proteins are not the actual bacterium, just something the bacterium produces). If a person has been exposed to TB, their immune system will recognize and attack the TB proteins, resulting in a hard, raised bump on the skin. This procedure is more invasive, subject to complications from existing conditions, and can still take 2-3 days for results. Urine samples have the advantage of being noninvasive (you're going to be peeing every 2-5 hours anyway), and the person doing the testing is never directly exposed to the bacterium, as can be the case with sputum samples.

While mass spectrometry was used to identify urine metabolites in this study, future point-of-care diagnostics may make use of electronic nose systems, which are currently being explored as a method of identifying volatile organic compounds and could potentially be developed as automated sensors for the specific volatile metabolites present in the urine of TB-infected individuals. This would streamline the procedure, make it more cost-effective, and provide a time advantage over other diagnostic methods currently being used. This would make a big difference in developing nations where skilled manpower, money, and resources are scant and where shortening the delay to diagnosis and treatment are key for reducing TB-related deaths.

1 In chemistry, a volatile compound is one that readily evaporates into the air. I was being facetious when I mentioned pee-sniffing in the title, but volatile compounds do make it to the nose more quickly... I'm just saying...

2 Would anyone be interested in a primer on how mass spectrometry works? It gets thrown around on TV procedurals a lot (CSI, Bones, etc.) and is depicted as a machine where you pump in a substance and it spits out all the molecules present in the sample. It ain't nearly that easy by a long shot.

Originally posted at Scientific American on August 8, 2011, where it was a Research Blogging Editor's Selection.

Banday, K., Pasikanti, K., Chan, E., Singla, R., Rao, K., Chauhan, V., & Nanda, R. (2011). Use of Urine Volatile Organic Compounds To Discriminate Tuberculosis Patients from Healthy Subjects Analytical Chemistry, 83 (14), 5526-5534 DOI: 10.1021/ac200265g

What can urine tell us?

Image credit: Flickr user Knowtex.
My urine has been tested for many things. For example, when I was offered my current job, my urine was tested for the presence of metabolites of illegal drugs. Drug metabolites are the breakdown products of various drugs, which remain in your blood until they are cleared by your liver or kidney and excreted in the urine. Because they stay in the body longer than the active drug, the window of detection is longer.

Last summer I had some liver problems, and my urine was detected for the presence of a whole host of different things that could give my doctors insight into my condition. It was tested for white blood cells, which are part of the immune system, and bilirubin, which is a by-product of the breakdown of red blood cells in the liver. An abnormally high concentration of either of these in my urine could indicate an infection or a hyperactive liver.

I’ve taken pregnancy tests that test my urine for the presence of an endocrine called human chorionic gonadotropin, or hCG. This endocrine is produced by the developing placenta of an embryo that has recently implanted in the uterine wall. This endocrine communicates with the corpus luteum, which is the now-empty follicle in the ovary from which the egg was released, telling it to continue to release another endocrine called progesterone. Progesterone is needed for the maintenance of the uterine wall during the pregnancy. Without the influence of hCG, the corpus luteum would die, eventually causing the woman to have her period. In my case, fortunately, my urine has always come back negative for levels of hCG that would indicate an implanted embryo. (I say fortunately because, trust me, I ain’t ready.)

My urine has been tested for the presence of a number of things throughout my life, all in the interest of medical, personal, or professional discourse. But humans are not alone in the venture of inspecting urine to learn more about themselves or others. Most people are familiar with the concept of pheromones, which are chemicals released as intraspecies messengers to elicit a social response. For example, the stinky urine that tomcats spray around their territory carries volatile compounds that send a clear message to other cats: This is mine. Stay away. The release of pheromones is to provide a benefit to the releaser and usually the receiver as well. When the tomcat sprays pheromone-laden urine, he benefits because it keeps away interlopers, and the potential interlopers benefit because they get to avoid a fight.

Tomcats use pheromones their urine to send messages intentionally, but sometimes the compounds in an animal’s urine can send unintentional messages. Arecent study in PNAS describes a compound in carnivore urine that helps prey species like mice and rats avoid predators. This compound, called 2-phenylethylamine (PEA), is something called a kairomone. Unlike pheromones, kairomones are interspecies messengers, allowing the receiver to ‘eavesdrop’ on the individual that left them behind. In the case of PEA, when rodents detect this kairomone, they know that a predator is in the area.

PEA triggers a rodent’s stress response and elicits avoidance behaviors that help the rodent escape predation by avoiding areas where there’s a lot of carnivore pee. Liberles and colleagues exposed rats to the urine of two different carnivores, isolated PEA, benzylamine (a chemical strongly related to PEA), and water. They found that the rats avoided the pure PEA and urine, but spent similar amounts of time around the water and benzylamine (see figure, adapted from the data in Liberles et al., 2011; click to enlarge), which suggests that rats show avoidance of PEA and can distinguish PEA from very similarly-related compounds. When PEA was enzymatically removed from lion urine, the rats no longer avoided it, spending similar amounts of time near the PEA-depleted urine as they spent near water. Similar experiments in mice show that the avoidance of PEA is dose-dependent, meaning that rodents will exhibit stronger avoidance behavior when the concentration of PEA is increased. Additionally, exposure to PEA provoked an increase in the circulating level of the rodent stress hormone corticosterone.

This is actually really cool because PEA is fairly ubiquitously present in the urine of carnivores and also relatively specific to carnivores as opposed to other mammalian species. As you can see in the chart (adapted from the data in Liberles et al., 2011; click to enlarge), many carnivore species have PEA concentrations in their urine that are an order of magnitude greater than those of rodents and other non-carnivore mammals. While rodents can also detect chemicals that are specific to the predator species that they encounter the most, their sensitivity to PEA allows them to recognize and avoid predator species that they have never even encountered before.

You might ask why carnivores have more PEA in their urine than other mammals do, but the answer isn’t clear at this time. There are a couple of possibilities, and the answer is likely a combination of the two. PEA is a metabolite of one essential amino acid found in dietary protein, so it may be that the sheer volume of protein in the diet is a contributing factor. It is also likely that carnivores have shared metabolic pathways that specifically produce PEA over other possible metabolites. Another possibility is that PEA might be produced in high concentrations to act as a pheromone in some carnivore species, and rodents adapted the ability to listen in on this pheromone as a kairomone.

Originally posted at Scientific American on July 25, 2011.

Ferrero, D., Lemon, J., Fluegge, D., Pashkovski, S., Korzan, W., Datta, S., Spehr, M., Fendt, M., & Liberles, S. (2011). Detection and avoidance of a carnivore odor by prey. Proceedings of the National Academy of Sciences, 108 (27), 11235-11240 DOI: 10.1073/pnas.1103317108

Growing pains! (or, Welcome Back!)

Being as how it is a brand new network, #SciAmBlogs is still figuring out its identity and its place in the science blogging community. As such, my blog Crude Matter is also developing, and I am currently trying to figure out what I want from it and what its role is supposed to be.

I dearly appreciate the increased readership and the massive amounts of support from Scientific American, but I also appreciate the concerns that my few regular readers have about the commenting situation over there. I also have to think about my own blogging desires. I like making personal, stupid, or frivolous posts from time to time, and I'm not comfortable doing that at Sci Am, seeing as how it gets indexed by Google News. :)

Have it AND eat it! Image credit: Flickr user Kimberly Vardeman.
As such, I've decided that I will continue blogging here at C6-H12-O6. I will cross-link the weekly(ish) meaty Crude Matter posts on the day they are posted and will re-post them here in their entirety after 24 hours. I realize I'm trying to have my cake and eat it too, but hopefully this situation will work out best for everyone. This way I can still have the personal blog while using Scientific American for outreach to a broader audience, and possibly funnel new readers to this blog.

If you don't give a rat's hiney about the other stuff and just want to read the straight up science, you should follow only the RSS feed for Crude Matter, which is here:

If you want to follow my personal blog and leap over to Crude Matter occasionally through the cross-link posts, you should follow the RSS feed for this blog, which is here:

If you want everything and the kitchen sink (recommended), follow both! If you follow me through Facebook/G+/Twitter, you don't have to do anything; this is only for people who follow me through bookmarks or feed readers.

And I do apologize for all the RSS hopping; although, I assume that if most of my readers are like me, they never deleted the old RSS from their feed reader anyway because they are incredibly lazy.

PS: I know things are a little dusty over here. Namely, all of my old images appear to be broken. This was due to a very unfortunate G+ mishap. (Protip: Don't delete the "blog photos" folder in G+ if you use it with the same gmail account that your blogger blog is associated with...) I'm going to try to fix this, but it may be unfixable.


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 ( If you have this blog bookmarked in your blogroll or internet favorites, please update to the new URL ( I look forward to seeing you there!

Image by Flickr user Andrew Huff.

7000 FPS video of water bubbles and droplets.

This is one of the craziest, most beautiful things I've ever seen. And I say that having just watched Black Swan for the first time last night, so, yeah.

I've been neglectful of this blog because of my new job, but I would be remiss if I didn't point out that the Pride edition of the Diversity in Science Blog Carnival was posted a few days ago at Denim and Tweed. I know June is over, but go check it out.