Below is a promotional video for the project that highlights Muhammad Ali’s struggle with Parkinson’s disease and his participation in 23andMe’s research program. If you or someone you know has Parkinson’s disease, watch the video, check out the website, and explore your options for participation.

With the support of a grant from the National Science Foundation and the National Institutes of Health, the American Chemical Society has developed a science activity kit for teachers to use with their students. This kit, titled Chemistry: Investigating your World, is being mailed to teachers who request it and meet the following criteria:

•               They plan to use the kit with a minimum of twelve 4th-8th grade students.
•               They request that the kit be sent to a school address within the continental United States.

Do you know a teacher who should know about this free chemistry kit?

If so, please forward the information below.

Request a FREE Science Activity Kit to celebrate the International Year of Chemistry 2011!

Although it’s now 2012, Chemistry: Investigating Your World kits are still available.  The kit is designed with enough materials for multiple classes of 12 to 32 students, working in groups of 4. The activities, reading level, and content are appropriate for students in fourth through eighth grades.

Request a kit at www.acs.org/iyckit.

Using the lessons in the kit, students will see demonstrations and do hands-on activities while investigating clues of chemical change, including:

·         Production of a gas
·         Formation of a precipitate
·         Color Change
·         Change in temperature

Check out the four lessons to find out how meeting scientists around the world, investigating clues of chemical change, and real-life applications make learning chemistry relevant and fun. Then be sure to request your free kit as soon as possible. Supplies are limited!

Black coffee: Probably what Paula Deen should have been drinking instead of all that sugar and trans fat.

Many of us, especially the current or former graduate students among us, are addicted to our breakfast caffeinated beverage of choice. Mine is tea, but if I had to guess, I’d wager that the most popular option is coffee. We chug it down in the morning to get ready for our day, we sip it thoughtfully at work, and we seek it out in the wee hours when we should be sleeping but instead we’re at the lab or at our desks, telling ourselves that we’ll run just one more gel or write just one more page. The ritual of coffee (or tea!) is deeply ingrained in our daily lives for many of us, but aside from keeping us alert, what else does it do for us? A recent study suggests that certain polyphenolic compounds in tea and coffee may offer protective effects against type 2 diabetes mellitus (T2 diabetes) by interfering with the formation of amyloid fibrils in the pancreas. Wow, that sounds great, doesn’t it? Another excuse to drink more of the stuff! But what the heck does it mean? In order to understand how this might work, we first need to understand some concepts. Specifically, what is an amyloid fibril, and what does it have to do with T2 diabetes?

Amyloids are deposits of proteins that have been folded in a specifically incorrect way (proteins must be folded properly in order to function properly). These misfolded proteins form aggregates (i.e., they clump together) that build up in tissues and cells, similar to the way that calcium deposits might build up in your pipes, for instance. You can see what this looks like in the photo to the left, which shows amyloid deposits (brown) of Abeta protein in the cerebral cortex. Amyloids tend to be associated with diseases such as Parkinson’s and Alzheimer’s disease in addition to T2 diabetes. The exact way that these protein deposits contribute to these diseases is unclear, but it is thought that their presence causes the tissues around them to be deformed, thus interfering with their ability to do their job. They may also cause cell death by interfering with the mitochondria, which are the organelles that supply cells with energy. In the case of T2 diabetes, the presence of amyloid fibrils in the pancreas is thought to kill the beta-cells that produce insulin. The amyloid fibrils in this case are made of a protein called human islet amyloid polypeptide (hIAPP, or amylin), which normally functions as an endocrine (i.e., hormone) that is released along with insulin from the beta-cells. Therefore, one way we can think about treating T2 diabetes is to stop hIAPP amyloid fibrils from forming in the first place.

Previous studies (in people of European and Asian descent) have reported that regular coffee-drinkers have up to a 50% lower risk of developing T2 diabetes than non-drinkers, but how might this work? One polyphenolic compound commonly found in tea, (-)-epigallocatechin 3-gallate (or EGCG), has been shown to have inhibitory effects on the amyloid formation of Abeta, alpha-synuclein, and hIAPP proteins, which are known to be associated with Alzheimer’s, Parkinson’s, and T2 diabetes, respectively. Coffee, like tea, has a host of polyphenolic compounds, such as caffeic acid (CA), chlorogenic acid (CGA), and their metabolites. It serves to reason that these polyphenols and related compounds in coffee may offer similar protective effects against amyloid formation and aggregation.

Caffeine, CA, and CGA are the three most abundant chemical compounds in coffee, so researchers from Huazhong University of Science and Technology, Wuhan University, and Wuhan Institute of Biotechnology (China) investigated whether they exhibited similar protective effects against amyloid formation as the tea polyphenol EGCG (published in the Journal of Agricultural and Food Chemistry). They exposed the amyloid-forming protein hIAPP to the tea polyphenol EGCG, caffeine, and the coffee polyphenols CA and CGA, and then they measured, among other things, the amount of amyloid fibrils that formed and the survival rate of exposed beta-cells from a rat cell line.

To the left are transmission electron microscopy images of hIAPP incubated with the compounds listed above (click to enlarge). I have edited the figure slightly to include labels. In part A, which had hIAPP alone, and parts C and D, which had hIAPP incubated with caffeine, you can see the fibrous amyloid protein bundles, which look a little bit like hairs or threads. Caffeine clearly was ineffective at stopping amyloid formation. In part B, EGCG appeared to stop amyloids from forming, as there were no fibrils detected, which is consistent with the existing research leading up to this study. In addition, both CA and CGA also inhibited amyloid fibrils from forming, with greater concentrations causing more complete inhibition. Small aggregates of hIAPP were detected, but they did not form mature bundles. So the coffee polyphenols do seem to stop amyloid fibrils from forming, similar to the tea polyphenol.

Does this inhibition result in less cell death? In fact, that does seem to be the case! The graph to the right shows the percentage of cells that survived when exposed to hIAPP alone or in combination with the study compounds relative to an untreated group of cells (the untreated group = 100% viability; click to enlarge). hIAPP alone caused the survival rate of beta-cells to drop by almost two-thirds, presumably because of the cytotoxic (i.e., cell-killing) effects of amyloid fibrils. In contrast, all four of the study compounds increased the survival rate to various degrees. EGCG (in a 1:1 ratio with hIAPP) and CA (in a 1:5 ratio with hIAPP) seemed to be the most effective at protecting the beta-cells at 75 and 96%, respectively. Perhaps the most interesting thing is that although caffeine did not stop the amyloid fibrils from forming, it still offered some protection against cell death! It could be that caffeine somehow alters the structure of the amyloid fibrils in a way that makes them less deadly to the beta-cells, even though it doesn’t stop them from forming entirely. It is also possible that caffeine interferes with the receipt of some of the chemical messengers involved in the cell death process.

These results show one potential way that drinking coffee may provide some beneficial effects against the symptoms of T2 diabetes. Polyphenols in the coffee probably slow or stop the formation of the amyloid fibrils, with caffeine itself also contributing to some degree. Slowing the aggregation of amyloid fibrils results in less beta-cell death, which means that the pancreas is less hindered in its ability to secrete insulin into the bloodstream after a meal. While the results weren’t shown in the paper, the authors also noted that the metabolites (i.e., the breakdown products) of CA and CGA showed similar anti-amyloid effects, meaning that even after CA and CGA are broken down chemically, the protective effects could still continue for some time.

Personally, I would be interested to know if ingesting significant amounts of sugar or cream with your coffee or tea would mitigate the benefits of these protective polyphenols. It may also be worthwhile to test the protective effect of coffee across a broader set of ethnicities, since some populations are more prone to developing T2 diabetes than others. Finally, it is worth pointing out that the cell viability study was conducted with rat cells, and therefore may or may not be indicative of what may happen with human beta-cells.

This doesn’t mean that your doctor will some day be prescribing you two extra cups of coffee per day to treat your diabetes, but it does mean that some of the compounds in your daily cuppa may wind up in diabetes medications in the future. All of that being said, drinking coffee should not be used as an alternative to seeking professional medical care for T2 diabetes or any other medical condition. The title of this post is somewhat tongue-in-cheek, because while many of us enjoy a cup or two (or five) of coffee or tea on a daily basis, it is not intended to cure or prevent any disease!

Cheng, B., Liu, X., Gong, H., Huang, L., Chen, H., Zhang, X., Li, C., Yang, M., Ma, B., Jiao, L., Zheng, L., & Huang, K. (2011). Coffee Components Inhibit Amyloid Formation of Human Islet Amyloid Polypeptide in Vitro: Possible Link between Coffee Consumption and Diabetes Mellitus Journal of Agricultural and Food Chemistry, 59 (24), 13147-13155 DOI: 10.1021/jf201702h

Image credits:

• (1) Coffee, via Flickr user Eric Heupel, licensed under Creative Commons license.
• (2) Amyloid deposits in the cerebral cortex, via Wikipedia user Nephron, licensed under Creative Commons license.
• (3) TEM images of hIAPP incubated with various compounds, reprinted with permission from Cheng et al. J. Agric. Food Chem., 2011, 59 (24), pp 13147–13155. Copyright 2012 American Chemical Society.
• (4) Viability chart of cells incubated with hIAPP and various compounds. Made by me using data from Cheng et al. J. Agric. Food Chem., 2011, 59 (24), pp 13147–13155. I know there are no error bars, as I did not have enough data to include them. They can be seen in the original publication.

Physiology

The wonderful quail… and what Sen. Coburn should learn about it and Cocaine and the sexual habits of quail, or, why does NIH fund what it does? Bora and Scicurious tackle the topic of another study that came under fire in Senator Coburn’s Wastebook.

What’s Inside: Enzyte Male Enhancer. It’s mainly just a bunch of stuff that promotes the production of nitric oxide, which is a vasodilator, meaning it causes your blood vessels to expand. Vasodilation in the penis contributes to an erection because dilating the vessels allows more blood to enter, leading to turgidity.

Pregnancy 101: On the cervical mucus plug and why I’ve never been more happy to hold something so disgusting in my hand. A great post on the role that mucus plays in female reproductive physiology.

The internal clitoris. You probably think you know where the clitoris is (I certainly hope you do), but it’s actually in more places than you’d think.

Will I get a yeast infection if I eat too much sugar? In a word, no. At least, not as long as you aren’t putting that sugar in your vagina.

Transfaunation and Fecal Transplants: What Goes Around Comes Around, Literally and Figuratively. I just LOVE a good blog post on fecal transplants. “We then discussed probiotics and he then told me an amazing story about how the old school farriers used a special method to treat horses if they were sick with some sort of gastrointestinal distress (e.g., colic). They would make the sick horse “poo tea” by taking feces from healthy horses and making it into a tea of sorts and then they served this to the sick horses.” POO TEA.

Other Science

Don’t drink the water! Why it’s okay but sometimes not okay to drink distilled water.

How a “designer baby” might just work. Although each of your parents contributes exactly 50% of your genome, the spread between grandparents is much more random due to segregation and recombination (i.e., rarely does each grandparent contribute exactly 25% of your genome). You could, in theory, choose gametes that favor the grandparent with a particular desired phenotype.

Doh! Top Science Journal Retractions of 2011. I remember a good number of these papers, but I did not know that many of them had been retracted.

Every drug is the ‘deadliest drug,’ especially oxycodone. “I’ve never heard an addict say, “my drug is the worst drug.” They know there isn’t such a thing. Such throwaway language stirs fear among those who may be medically prescribed oxycodone and creates a never-ending dark tunnel for those who may already be abusing the stuff.”

Everyday Science: Why Can You Hear Around Corners But Not See? A nice discussion of the difference between light and sound waves.

The Barry White Syndrome: Why are deep voices attractive? I hate having to limit myself to only one Anthropology in Practice post per link round-up because her posts are always so interesting and relevant. Alas.

Other Stuff

The colors of a family. “I was holding my 1-year-old, ambling about downtown with some friends. White friends. She must have thought my boy belonged to one of them. There’s a simple explanation: I’m black but my son, Ashe, is white. At least he looks it. But things are more complicated than that.”

World’s first pee-controlled video game opens in London bar. Pee left, ski left. Pee right, ski right. This is nice, but I want a version in the women’s restroom too.

13 Myths and Misconceptions about Trans Women. This post is actually in two parts; don’t forget to click the link to the second part at the bottom.

The Arkh Project. This is a fantasy RPG computer game in the early stages of development, made by queer people of color and featuring queer people of color as the main characters (the protagonist is a biracial feminine genderqueer deity named Ain/Aina). There’s concept art and preliminary story lines and game play, but they need visibility, promotion, and donations (ChipIn or Indiegogo (preferred)) in order to produce the game. If this is up your alley at all, you should consider tweeting, linking, or donating. [I have no financial interest in this game. I'm promoting it simply because I think it is an excellent idea and something that needs to be made. Also the protagonist is cute beyond words.]

The History of the New Year. “If circumcision doesn’t say start your calender year, I don’t know what does.”

The phenomenon isn’t restricted to domesticated cats, either:

Cats aren’t the only animals that are mentally stimulated by flashing and dancing lights, though. As it turns out, researchers at Wageningen University, in the course of their research on ethical livestock farming, noticed that pigs like to play with dancing lights as well. European regulations currently require that pig farmers provide mentally-stimulating activity for their pigs in order to reduce boredom, which leads to aggression and biting, and researchers at Wageningen University, in collaboration with the Utrecht School of the Arts, are currently developing a video game called “Pig Chase” for livestock pigs that is not unlike my cat’s iPad app.

The key difference, however, is that this game would be an interspecies two-player game. [EDIT: I was contacted this afternoon by Nate at Hiccup, and he informed me that Game For Cats has also recently incorporated interspecies functionality. I didn't know that, so thanks for the update!]

The researchers discovered that farm pigs responded to a wall of dancing lights by chasing the spots of light with their snouts. This provoked them to pose the question of whether humans and pigs could interact collaboratively in a game format. The human would control a ball of light remotely via a touchpad (such as an iPad or tablet computer) and try to attract the attention of the pig long enough to move a ball of light into a target, which would light up the wall in a celebratory fireworks-like display.

The value of the game as entertainment and mental stimulation for pigs is as of yet untested, but the researchers hope that their project will open up new questions in debates about animal farming and welfare in the digital age, as well as opening up new venues for research on animal cognition and behavior. For more information on the Playing with Pigs project and Pig Chase, check out their website.

Featured image credit: Wageningen University and Utrecht School of the Arts.

EDIT (Jan 15): On the subject of video games, I’m promoting a video game in the early stages of development called the Arkh Project. It is a fantasy RPG video game featuring queer people of color as the main characters. They are currently seeking donations and link-sharing to generate visibility for the project. Visit their website or see the bottom of my latest links post for more information, if you are interested. [I have no financial interest in this game. I'm promoting it simply because I think it is an excellent idea and something that needs to be made. Also the protagonist is cute beyond words.]

The policy has provided access for physicians and their patients, teachers and their students, policymakers and the public to hundreds of thousands of taxpayer-funded studies that would otherwise have been locked behind expensive publisher paywalls, accessible only to a small fraction of researchers at elite and wealthy universities.

The policy has been popular – especially among disease and patient advocacy groups fighting to empower the people they represent to make wise healthcare decision, and teachers educating the next generation of researchers and caregivers.

But the policy has been quite unpopular with a powerful publishing cartels that are hellbent on denying US taxpayers access to and benefits from research they paid to produce.

[...]

So I urge you to call/write/email/tweet Representative Maloney today, and tell her you support taxpayer access to biomedical research results. Ask her why she wants cancer patients to pay Elsevier $25 to access articles they’ve already paid for. And demand that she withdraw H.R. 3699.

Representative Maloney:

Twitter: @RepMaloney @CarolynBMaloney

Phone: 202-225-7944

FAX: 202-225-4709

Email: Use this form

EDIT: Thanks to commenter Cogitari for pointing out something I originally meant to put in this post, which is that writing to your OWN congressperson may be your best bet at getting a response. You can find your congresspeople by going to house.gov and senate.gov and using the search tool in the top right corner of each.

My fellow SciAm-blogger Janet has a post up discussing the ethical issues involved in the proposed act:

Let’s take this at the most basic level. If public money is used to fund scientific research, does the public have a legitimate expectation that the knowledge produced by that research will be shared with the public? If not, why not?

Kevin Zelnio has a good discussion of the topic up on his blog, and there’s also a roundup of blog posts on the topic here.

The Evolutionary Errors of X-Men

Failed Flaxseed and Bad News Brownies

Mock Missive: World Association of Organic Chemists limits use of “organic”

The Revolutionary New Birth Control Method for Men

“Homophobia Is Apparently Associated With Homosexual Arousal”

Eating mussels can make your semen radioactive!

The mental burden of a lower-class background

Comparative Physiology Crystal Ball

The Treasures of Urine

Personal genomics: no longer just for white folks

Scientific Advances on Contraceptives for Men

Dolphin may sense the body electric

Out-Of-The-Blue Panic Attacks Aren’t Without Warning: Body Sends Signals for Hour Before

Will Carrots Help You See Better? No, but Chocolate Might

Recovering from grad school

Circumcise or Don’t? Quandary for Parents

CT Scans of Baby Mammoths Reveal Ice Age Mystery

My Chemically Fueled Life

You Become as You Eat

How Probiotics May Save Your Life

Image credit: Flickr user Anders Adermark via Creative Commons license.

Instead of reviewing my activities in the past year, I thought I’d do something a little different and share with you the blog posts and news articles from 2011 that I found the most memorable. Because there are so many, this post contains links from January through June. If I remember to do a part two, that list will undoubtedly be shorter because I started my current job in June and have had much less time for blog and news reading.

Browse, read, and enjoy. Glancing over this list, I think it probably tells you a thing or two about where my greatest interests lie.

AT&T Pretty Much Predicted 2011 in 1993

Kissing & the science of humanity

Lemur Week: Ringtailed Lemurs Look Where You’re Looking

Hard Core

The Mathematics of Beauty

No love for outsiders – oxytocin boosts favouritism towards our own ethnic or cultural group

Stop using the word “Caucasian” to mean white

How the diabetes-linked ‘thrifty gene’ triumphed with prejudice over proof

Saturday Evening Rant, Iodine Edition

Are your Allergies worst in the morning?

Extra nipples – They’re just a matter of timing

Did Henry VIII have a blood disorder?

Masturbation calms restless leg syndrome

The danger of appealing stories: anecdata, expectations, and skepticism

Is Bigger Really Better?

Forget chocolate on Valentine’s Day, try semen, says Surgery News editor. Retraction, resignation follow

The “Lesbian Until Graduation:” Now A New York Times Most Emailed Article!

That’s Not a Dinosaur!

The Neuroscience of the Gut

Sucked Out Of A Plane?

Nervous Nellies

Reflections of Gotham: Why Do New Yorkers Wear So Much Black?

That (expletive) Semen-Antidepressant Study

Divided by language, united by gut bacteria – people have three common gut types

Nature’s Living Tape Recorders May Be Telling Us Secrets

How peppermint may cool that irritable bowel syndrome

Superfetation: Pregnant while already pregnant

Sex on the brain: Orgasms unlock altered consciousness

Marketing food to kids with cartoon characters

Gut Bacteria Linked to Behavior: That Anxiety May Be in Your Gut, Not in Your Head

Mpemba’s baffling discovery: can hot water freeze before cold? (1969)

Bats Use Carnivorous Pitcher Plant as Living Toilet

Blue Lights Shown to Give a Brain Boost! But is a Better than Coffee?

Semen allergy suspected in rare post-orgasm illness

Researchers at the University of California-Riverside have pushed the mission of the National Science Foundation to new limits. In 2011, they received an NSF grant of almost $150,000 to create a video game called “RapidGuppy” for cell phones and other mobile devices. In the game, targeted for students 12-21 years old, users control the growth and evolution of a guppy. Students can gain insight into the environmental factors that cause the fish to adapt. To reach the public, the researchers will use “[a]n extensive social media campaign,“ which they see as increasing the public level of interest in evolution, genetic change, and science careers. Using taxpayer dollars, “RapidGuppy” might soon be on Facebook, right alongside “FarmVille” and “Scrabble.”

The first thing I noticed upon reading this is that Senator Coburn understands neither the scope of the project nor the science behind it. He says that users will “control the … evolution of a guppy”, but anyone who has taken an introductory biology class knows that evolution is something that happens over generations and is not something any one guppy can do. You may say that this could be an honest mistake or just being ‘lazy’ in communicating the gist of the project, but in my opinion it shows that either he doesn’t understand the science that he is bashing or he doesn’t mind spreading misinformation to his constituents. I have to wonder whether or not there’s more than a little bit of anti-evolution sentiment behind the reasons why this particular project made his list.

He also fails to mention that the educational game will be linked to a website that shows videos, photos, and descriptions of actual evolution and ecology research being conducted by the scientists involved in The Guppy Project. He misleads you into thinking that the sole purpose is to make a video game, but in actuality the video game will serve to generate interest in evolution and ecology and funnel those interested parties into the actual research. Given the age group being targeted, this is an excellent strategy to slowly acclimate young science students from the abstract ideas of “adaptation” and “evolution” to what those terms mean in application, and then to what that sort of research really looks like.

“Video games” in the classroom are nothing new. I grew up with Math Blaster, Mario Teaches Typing, and other video games (including one awe-inspiring oceanography game whose name eludes me at the moment) being used more and more as computers began to infiltrate the classroom in the mid-1990s. Now students can use mobile apps and online games to dissect frogs, explore their anatomy, learn the life cycle of a star, and explore other topics that would otherwise be too difficult (due to rarity, location, or ethical reasons) or too abstract to touch with their bare hands. This may just be my own opinion, but I do not believe that it is wasteful to invest in the STEM education of our middle schoolers, high schoolers, and college students. Apparently Senator Coburn disagrees.

Image: Male and female guppies, Poecilia reticulata. Image credit: Marrabbio2, Wikimedia Commons.

This video describes the physiology behind how pimples form. In short, excess sebum (or skin oil) clogs a pore and traps dead skin cells inside. Bacteria proliferate inside the pore to feed on the trapped skin cells. White blood cells migrate to the pore to fight the bacterial infection, and the mix of dead skin, white blood cells, and bacteria form the pus core of the pimple. The video also has a great explanation of the chemistry behind how benzoyl peroxide fights the acne-causing bacteria.

Image credit: NIH, via Wikimedia Commons.

Philip Burne-Jones, The Vampire, 1897

The curse of the Halloween baby: women avoid giving birth on ‘evil day’ and Are Pregnant Women Subconsciously Avoiding Giving Birth on Halloween? A recent study comparing birth rates on Halloween vs. Valentine’s Day suggests that pregnant women may be able to exert some subconscious control over the timing of parturition (i.e., when they give birth). It is possible that the negative connotations associated with Halloween may affect the mother’s endocrine levels and thus affect the timing of labor as well; however, the potential  mechanism is unknown.

Here on #SciAmBlogs, Cassie Rodenberg (Dear Dracula, Edward Cullen and Bill Compton: you have a substance abuse problem) and Eric Michael Johnson (A Natural History of Vampires) both blog about the association between vampires and various actual diseases such as rabies.

The Blogfather Bora blogs about how an upset in circadian physiology explains many symptoms of zombism in his post, Are Zombies nocturnal?

Just in time for Halloween: Vampires Dr. Doolittle has another take on the vampire/rabies situation by including an extra factor: vampire bats as vectors!

Brian at Dangerous Experiements discusses the physiology of the fear response in his post, How film makers are using your own imagination to scare you.

If you know of any other physiology-related Halloween posts from this weekend or today, send me the link via comment, email, or tweet, and I’ll add them to the list!

Making hard candy. Credit: Flickr user taygete05.

Some things of note:
(1) Hard candy is technically a glass made of sugar!
(2) There are three stages of sugar boiling, and the maximum temperature that it reaches determines the physical properties of the resulting candy (I think this is primarily a function of how much water is remaining in the sugar mixture).
(3) If you watch the video, you’ll figure out why hard candy always has a ring around the edge. This was something I didn’t know.

Enjoy. Perhaps I’ll write a post later about what your body does with all that sugar after you eat it.

For Cave’s Art, An Uncertain Future

The cavern that houses Spain’s most celebrated prehistoric art is on the mend from a microbial infestation that closed it to the public. A push from regional government officials to reopen Altamira Cave to visitors has researchers who worked to improve its condition worried that their efforts will be undone (Science, DOI: 10.1126/science.1206788). But like the bacterial colonies dotting the storied cave’s walls, the scientific and ethical issues that will determine its fate are colored in shades of gray.

Nestled underground near a village in northern Spain, Altamira Cave contains astonishingly lifelike renderings of fawns, horses, and bison painted on its ceilings. The multicolored likenesses, more than 14,000 years old, are recognized as a pinnacle of Paleolithic rock art. The United Nations Educational, Scientific & Cultural Organization (UNESCO) declared Altamira Cave a World Heritage Site in 1985.

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). 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.

If you don’t want to jump through the hurdles of Scientific American’s current commenting system, you can leave a comment over at my other blog.

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.”

Earlier this week I shared the story of my specific phobia of vomiting, and today I’m going to blog about an article recently published in PNAS (open access!) about the efficacy of cortisol supplementation during exposure therapy for specific phobias.

Cortisol, which I have blogged about before, is a major endocrine involved in the human stress response (corticosterone, a closely-related steroid, serves the same purpose in many other animals). Stressful experiences are also learning experiences for many individuals (“I’ll never do that again…” etc.), and cortisol seems to have an impact on the building and retrieval of memories. Specifically, it appears to promote the storage of new memories while simultaneously repressing the retrieval of already stored memories. This makes it a potentially beneficial supplement during exposure therapy, which is based on replacing traumatic memories of objects, events, or situations with repeated non-traumatic exposures to “unlearn” the fear.

In this study, the authors compared two groups of people undergoing exposure therapy for their fear of heights: a control group that received a placebo and an experimental group that received 20mg of cortisol one hour before their treatment sessions. (The two groups did not differ in baseline levels of cortisol, and the experimental group did have higher levels of circulating cortisol, both validated by saliva samples.)

Exposure therapy reduced self-reported fear in both groups, but the effect was amplified in the cortisol group, both 3-5 days after treatment and at follow-up a month later. This suggests that cortisol supplementation increases the efficacy of exposure therapy in people who have specific phobias of heights. However, more studies need to be done to see if the cortisol treatment has continuing long-term effects in the fear response.

I hesitate to jump for joy because I have no idea if exposure therapy (with or without cortisol) would be effective or even possible for my specific phobia. I am not sure how well these results can be extrapolated to other specific phobias, although previous research suggests it may also be beneficial in arachnophobia and social phobia.

de Quervain, D., Bentz, D., Michael, T., Bolt, O., Wiederhold, B., Margraf, J., & Wilhelm, F. (2011). Glucocorticoids enhance extinction-based psychotherapy Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1018214108

I have a specific phobia of vomiting. I don’t like to talk about it in my online life because it is a major source of stress in my offline life (it is the root of my agoraphobia), but I bring it up today because I have some unanswered questions that I’d like to put out into the blogosphere.

For those of you who are not familiar, I will try to outline the nature of emetophobia, at least the way I experience it. It stems ultimately from a fear of losing control of one’s body. Vomiting is unavoidable, violent, and sometimes unpredictable. It isn’t fun for anyone (well, almost anyone), but for an emetophobe it becomes a life or death situation. That loss of control is not just unpleasant, it is entirely unbearable and intolerable, and the mere thought of losing control in such a manner is enough to arouse panic and hysteria. As a result, an emetophobe becomes hyperalert to internal and external cues that vomiting is about to happen. Internal cues like nausea, or external cues like someone else actually vomiting, saying they don’t feel well, saying they had vomited recently, etc. It differs from person to person, and some people are only afraid of themselves vomiting whereas others are afraid of themselves and others vomiting. To speak for myself, the only reason why I’m afraid of someone else vomiting is because I’m afraid I’ll catch whatever they have and, as a result, vomit myself.

As a result of this state of being hyperalert, there are undoubtedly a lot of false positives. Emetophobes are notorious for not being able to decipher their own gastrointestinal cues. Non-pathological sensations like having gas or feeling full are misinterpreted as nausea. Nausea (real or perceived) causes anxiety, and one of the symptoms of anxiety is, yeah, more nausea. It becomes a terrible positive feedback loop that can be really hard to escape once the ball is rolling.

I have several coping mechanisms that I use when I feel the anxiety beast starting to swell inside me. They fall into several categories: preparative, preventative, and distractive. Preparative behaviors are things that will ease the process if I actually do throw up, such as taking off loose clothing, tying back my hair, and making sure I have access to a toilet. Preventative measures are things like taking antiemetics, benzodiazepines, sipping water, sucking on peppermints, etc. The distractions, however, seem to be the most effective.

My distraction techniques usually have two horns: giving my body a menial task to accomplish and giving the rest of my brain something to focus on. Generally this involves walking around my apartment and either having a conversation with my boyfriend (if he’s around and willing to oblige) or putting something light and fluffy on the TV. I’m fond of sitcoms and baking shows (like Cupcake Wars) for this situation. The TV/conversation part is easy to understand: I’m providing an easy distraction for my brain to focus on instead of thinking about the nausea and anxiety. If I don’t focus on it, most of the time it will go away on its own. The walking part is less easy for me to understand.

I know that having a menial activity to focus on is part of the distraction process. If I’m focused on walking around and balancing, even if only a tiny part of my brain is involved, that’s one less bit of my brain that can be thinking about my stomach. But, that’s not the only thing. The walking actually jostles my body, and adds “noise” to the internal cues that I’m misinterpreting as nausea. The walking seems to literally settle my stomach by covering up the stimulus with other sensations. But finally, I can’t fully rule out a physiological connection. Could there be a chemical reason why walking settles the stomach or reduces anxiety? I’ve heard of “walking through the pain”, but can you walk through the fear as well? I don’t know enough psychology or neuroscience (I imagine the brain-gut axis is very important in this response, but I don’t know how) to know the answer to that, so I’m hoping that someone out there will. Can physical movements calm the sympathetic response?

As a side note, I have often wondered if there was a physiological reason why emetophobes claim to vomit less often than normal people. I know that the sympathetic response causes gastrointestinal motility to slow down. If fear slows down peristalsis, could it also slow down reverse peristalsis?

BOSCHEN, M. (2007). Reconceptualizing emetophobia: A cognitive–behavioral formulation and research agenda Journal of Anxiety Disorders, 21 (3), 407-419 DOI: 10.1016/j.janxdis.2006.06.007

Davidson, A., Boyle, C., & Lauchlan, F. (2008). Scared to lose control? General and health locus of control in females with a phobia of vomiting Journal of Clinical Psychology, 64 (1), 30-39 DOI: 10.1002/jclp.20431

Lipsitz, J., Fyer, A., Paterniti, A., & Klein, D. (2001). Emetophobia: Preliminary results of an internet survey Depression and Anxiety, 14 (2), 149-152 DOI: 10.1002/da.1058

Veale, D., & Lambrou, C. (2006). The Psychopathology of Vomit Phobia Behavioural and Cognitive Psychotherapy, 34 (02) DOI: 10.1017/S1352465805002754

This is a slightly revised version of a post at Field of Science on April 22, 2011.

Earlier this year I received Get Me Out: A History of Childbirth from the Garden of Eden to the Sperm Bank by Dr. Randi Hutter Epstein through a Science Online 2011 giveaway contest on Twitter. It took me a while to get around to reading it, partially because I was busy churning out my thesis at the time, but also because it wasn’t a topic I found entirely interesting. I am not interested in being pregnant at this point in my life, so a book about childbirth isn’t on my radar right now. However, I decided to keep it around because you never really know what the future may bring. As it turns out, last week I had a very disturbing nightmare about being pregnant and being forced to have an abortion. The dream continued to disturb me a few days after the fact, so I grabbed the book off my bookshelf and started to read, thinking that it might help displace the “bad taste” of the dream.

Epstein has a nice light touch to her writing, so what could easily have been a dense and difficult book was actually very smooth and palatable. I banged it out in two days and it definitely achieved the desired effect of getting my mind off of the nightmare. The book is organized into five parts:

The first part covers the history of childbirth up to the 20^th century. The focus is mainly on the invention of forceps and the contributions of Dr. Marion Sims, who is lauded for developing a surgical method to fix vaginal fistulas (a painful complication of childbirth where the vaginal wall tears and opens into the bladder or rectum) and simultaneously abhorred for developing his method through what essentially amounts to the torture of slave women.

The second part covers the move from bedroom to hospitals. Puerperal fever was a leading cause of post-partum death among mothers before the discovery of germs, which doctors transmitted freely between women in hospitals. This led to the bizarre practice of letting women’s genitals “air out” on the roof of hospitals for days after giving birth, thinking that this would keep the mother from getting sick. After the establishment of sanitation came more drugs, and a chapter is devoted to “twilight sleep”, the first attempt to use drugs to ease childbirth.

The third part explores the role of psychology in conception, the natural childbirth movement, and the devastating consequences of certain fertility drugs. The fourth part covers C-sections, freebirthers (an even more radical take on natural childbirth), and sonograms, and the fifth part covers gamete donation and cryopreservation.

Running themes throughout this book include the battle against midwives by medical doctors, the battle against medical doctors by pregnant women, and the rapidly oscillating opinions on what role drugs should play in pregnancies and childbirth. It seems that throughout history, doctors have been attempting to discredit midwives (both out of concern for women’s well-being, but also in order to take over their business), women have been at odds with doctors over what is best for their pregnancies, and women have been unable to agree with each other over whether or not to take drugs, and which types of drugs, and the reasons to use or not use a particular birthing method. There are millions of different ways to have a child, and nobody can agree on anything! No wonder mothers are so stressed out.

One thing about this book that bothered me is that the book claims to be a “history of childbirth”, but it is more accurately described as a history of childbirth in the western world. The book is not without the occasional reference to things happening in the non-western world, but the book is clearly focused on Europe and America, and largely devoid of Asian or African history and practices. This is not necessarily a bad thing or a criticism of Epstein’s work. The book is clearly marketed towards western women, so there’s no shame in focusing on western history (and to include a worldwide picture of childbirth throughout the ages would have made the book much longer and probably not as easy a read). I just believe in being honest about the limitations of scope, that’s all.

While Epstein strives to write a fair and balanced book, sometimes her biases do slip in to the narrative. This is particularly obvious in the chapter on freebirthers, who believe in giving birth without any medical help at all. Her language in this chapter tends towards the dismissive at times, but I suppose that’s to be expected, given that she’s a medical doctor. To be fair, even scientist women aren’t in 100% agreement about the level of medical intervention that is best for a pregnancy and birth. See, for example, Dr. Isis and Kate Clancy‘s recent posts on the subject. On the whole, though, her stance is clear. There’s no one way to have a baby; women should decide what is best for them based on the information available, and then stick to their guns. And, perhaps just as importantly, when a mother chooses one method, it does not inherently translate into her making a judgement against mothers who choose other methods. New mothers have enough to worry about without being paranoid about how others will judge them based on their choices.

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 here. Many readers are put off by the login requirement, and hopefully they will be appeased by the Twitter/Facebook login system that we will be getting soon.

I also have to think about my own blogging desires. I like making personal, stupid, or frivolous posts from time to time, and that isn’t something I’d be comfortable doing here 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 at my other blog, C6-H12-O6. My shorter, lighter posts will go there (to reach my old readers and community), and my meatier posts will go here (for the wider audience and attracting new readers). I will cross-link the meaty posts over at C6-H12-O6 on the day they are posted here and will re-post them 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.

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 this blog, which is here: http://rss.sciam.com/crude-matter/feed

If you want to follow my personal blog and leap over to this blog occasionally through the cross-link posts, you should follow the RSS feed for C6-H12-O6, which is here: http://ecophysio.fieldofscience.com/feeds/posts/default

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.

Giant clams: Delicious. Also stinky. Image credit: Wikimedia.

Hill got into studying coral bleaching as a bit of a happy accident. He was doing work on giant clams in the south Pacific, investigating why the giant clams took on a foul odor a few hours after being killed. The locals had undertaken a major operation to farm and sell the giant clams around the world as delicacies (apparently they’re very delicious), but even when frozen, the clams were inedible after a few hours because of the breakdown of a chemical called dimethylsulfoniopropionate (DMSP) (which Hannah blogged about recently over at Culturing Science). The clams are symbionts with a species of algae that produce very large quantities of DMSP, and as a result, the DMSP settles in their bodies in quantities that are orders of magnitude larger than similar marine animals. After the animal dies, the DMSP breaks down, and one of the by-products is dimethylsulfide, which is responsible for the rank odor of the clams. The happy accident happened when Hill began using mass spectrometry to confirm the presence and by-products of DMSP in the clams. One of the mass spectrometry specialists that he worked with commented on the fact that there were multiple types of betaines in the clams as well.

Betaines are well-known to exist in various plants, especially crop plants, many of which have been genetically engineered to express more betaines. From my understanding, betaines can act as osmolytes (compounds that affect the diffusion of water through membranes) and help protect membranes and proteins from various stressors. In plants, this generally means protecting photosynthetic pathways from high temperatures and high levels of radiation from the sun during the peak of the daylight cycle. You would think that more sunlight would be good for photosynthesis, but apparently it is the opposite because of the negative effect of irradiation. As a result, there is often a dip in photosynthetic productivity in the afternoon (a phenomenon called photoinhibition), unless the plant can shield itself from harmful irradiation using betaines.

A partially bleached coral. Image credit: Wikimedia.

This information is relevant to corals because of the decline in coral populations due to bleaching. ‘Bleaching’ occurs when corals lose their algal symbionts (which are what give corals their brilliant colors) because of high water temperatures and high light intensity. When the symbionts leave or die due to photoinhibition, it is more difficult for the corals to survive. While corals were known to contain betaines for osmotic protection, the potential role of betaines in the stabilization of coral photosynthetic pathways had been largely ignored until recently. With this in mind, Hill and colleagues set out to determine the ecological patterns in coral betaine concentrations, which would be quite valuable for informing future conservation efforts.

Hill found that colonies of corals at shallower depths had higher concentrations of betaines than colonies in deeper waters and that colonies living in exposed areas had higher concentrations of betaines than shaded colonies. This is good supporting evidence that betaines are suppressing photoinhibition in corals, because exposed colonies and colonies in shallower water experience higher water temperatures and higher levels of radiation than their deeper or shaded counterparts. In addition, they found that betaine levels were higher in the afternoon than in the morning, suggesting that betaine levels were susceptible to phenotypic plasticity in response to more direct sunlight.

Hill is currently investigating the function of the betaines in these corals, to determine whether or not they are actually stabilizing photosynthesis in corals as they do in vascular plants. He is also investigating whether or not the betaines are being produced by the corals themselves, or by the algal symbionts, or both.

Hill, R., Dacey, J., Hill, S., Edward, A., & Hicks, W. (2004). Dimethylsulfoniopropionate in six species of giant clams and the evolution of dimethylsulfide after death Canadian Journal of Fisheries and Aquatic Sciences, 61 (5), 758-764 DOI: 10.1139/f04-029
Hill, R., Li, C., Jones, A., Gunn, J., & Frade, P. (2010). Abundant betaines in reef-building corals and ecological indicators of a photoprotective role Coral Reefs, 29 (4), 869-880 DOI: 10.1007/s00338-010-0662-x

Food waste in the land of “Man vs. Food” by David Wogan. “Food waste at consumer level in industrialized countries (222 million ton) is almost as high as the total net food production in sub- Saharan Africa (230 million ton).” Nearly half of the edible food produced in the USA is never eaten.

You become as you eat by Razib Khan. Biology influences culture, and culture influences biology. Agriculture and animal husbandry changed what and how we eat, but our digestive physiology also had to adapt to process things like wheat and dairy.

How probiotics may save your life by Rob Dunn. Probiotics are thought to help many digestive ailments, but the actual data to support these claims are slim, and the physiological mechanism for how they might work is still unknown. However, recent research in mice shows a potential mechanism for how one probiotic strain can out-compete harmful H. pylori in the gut.

Will carrots help you see better? No, but chocolate might by Cheryl Murphy. Experimental data suggest that flavonols in dark chocolate increase vision and cognitive performance. I have a post about chocolate in the works for next week as well.

Organic honey is a sweet illusion by Alex Wild. “A standard jar of honey from the supermarket requires bees to make a million flower visits. A colony might produce 50 to 100 such jars per year.” Because honey production requires so many flowers, bees often stray up to 5 km from their hive when foraging for nectar, and when resources are scarce they can double their radius. It is beyond the power of many organic farmers to restrict the use of pesticides within such a large radius of their hives.

I mean, I'm sure that's *supposed* to be water in her glass, but it looks like... no... I won't go there. Image credit: Library of Congress via Wikimedia Commons.

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.

Mycobacterium tuberculosis under scanning electron micrograph. Image credit: Centers for Disease Control and Prevention via Wikimedia Commons.

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.

M. tuberculosis culture showing growth of colonies. Image credit: Centers for Disease Control and Prevention via Wikimedia Commons.

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.

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

Dear Michelle,

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To show our appreciation and to encourage others to join in this research revolution we are giving you a $50 coupon that you can share with as many people as you like. This coupon expires in 7 days (August 9, 2011) so make sure you get the word out fast.

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Use coupon code "B8KYDH" at checkout to get $50 off your kit.

I highly recommend 23andMe’s genotyping service, so I’m happy to pass on the savings to you. I also highly suggest using the various aftermarket services that are available once you’ve gotten your results and downloaded your data. I plan on re-posting some of my adventures with using aftermarket genotyping services, but you can also browse them at my old blog.

Not really what chemistry is all about. Image credit: Flickr user Horia Varlan

I’d like to start the day off with a discussion about the common misconception that chemistry is all about test tubes filled with colorful liquids (and sometimes it is; as a grad student I worked with cupric acetate, which in solution turns a beautiful and brilliant blue) and boring stuff like p-orbitals (sorry to anyone out there who actually gets jazzed by orbitals), and it can’t possibly have anything to do with <insert your field here>. I think this might be a big reason why outsiders don’t really notice how ubiquitous chemistry blogging really is.

As I mentioned in my introductory post, I work for the American Chemical Society. (It just so happens that 2011 is the International Year of Chemistry, something which the ACS is, understandably, very excited about.) ACS’s tagline is “chemistry for life”, and our mission includes a commitment to “improving people’s lives through the transforming power of chemistry”. I find this message particularly apt, because our lives are inextricably linked to chemistry in countless ways that we take for granted every day. To bring the message home, this is a physiology blog, and physiology is not immune to this phenomenon! In fact, it can be a wonderful example of how biologists use chemistry every day without really thinking about it.

Your body runs on chemistry. There’s no two ways about it. To bring it down to the molecular level: your body is an aqueous environment. Your cells are merely bags of fluid floating in even more fluid. The movement of various ions and molecules into, out of, and between your cells is what causes almost everything that happens in your body. Here are some molecular approaches to thinking about the biochemistry in some of your favorite science blogs:

Action potentials in your nerve cells are responsible for carrying information to your brain from your sensory systems and sending instructions from your brain back out to your organs and muscles. These action potentials are electrical messages, driven by the movement of sodium and potassium ions (ions… you know, chemicals) into and out of the cell membrane of the neuron axon. Once the signal reaches a synapse, the message is converted to a chemical message in the form of a neurotransmitter, which crosses the synaptic cleft to trigger a new action potential in the next nerve cell down the line. A neurotransmitter is just another tiny molecule with an enormous impact on our well-being. So many essential parts of our being are the result of all of this brain chemistry, from our sensory perceptions and our compulsive desires to our sense of self and perception of others and how we fit into our world.

Our reproductive systems are awash with chemicals as well. What many people know as “hormones” are more accurately called endocrines, which are molecules that can be very similar to neurotransmitters (some neurotransmitters also function as endocrines), but they travel through the blood to impact many parts of the body instead of just the next cell down the line. The classic hormones that many people are familiar with are the sex endocrines such as testosterone and estrogen. Both of these belong to a class of endocrines called steroid endocrines, which are all derivatives of a cholesterol molecule. The results of these endocrines that we can see are the secondary sex characteristics of men and women; endocrines drive the deposition of fat in the breast and hips of women and the building of muscle in men. They also have results that we cannot see but definitely experience; two other endocrines called follicle stimulating hormone and luteinizing hormone are responsible for the production of sperm in men and the maintenance of the monthly cycle of women (along with estrogen and progesterone). None of these wonderful (and sometimes not-so-wonderful) things would happen unless we had all these chemicals floating around in our bloodstream.

Speaking of endocrines, melatonin is another chemical that helps drive our circadian rhythms. Melatonin is secreted by the pineal gland of the brain in the absence of blue-wavelength light and is part of the feedback system that causes you to feel drowsy when it is dark outside. Your genes run on chemistry also. Gene expression is often the result of converting strings of nucleic acids into proteins made of strings of amino acids, all of which are chemicals! Your cardiopulmonary system is a chemical superhighway! Not only does the blood carry all the endocrines I discussed earlier, but it also carries oxygen and carbon dioxide back and forth between the lungs and your body tissues. Carbon dioxide dissolves in the blood plasma to form bicarbonate and hydrogen ions, and the extra hydrogen ions make your venous blood more acidic than your arterial blood. This is very relevant to your well-being, because if you can’t get rid of that carbon dioxide at a quick enough pace (for example, if you’re working out strenuously and your breathing rate can’t keep up with your rate of converting oxygen to carbon dioxide), you develop respiratory acidosis and puke on the sidewalk. Puking causes you to off-load a ton of stomach acid (digestive system chemistry!), which then gives you metabolic alkalosis. Your body’s pH is always at a delicate balance, and your circulatory and respiratory systems are at the heart of it all (err, no pun intended).

To make a long story short (too late), chemistry is relevant to all of us earthly beings. As the beloved nerd comic strip xkcd put it so aptly (though not in as many words), life itself is just applied chemistry.

Take some time today to think about the chemistry of your body. Every sensation you perceive, every movement you make, every involuntary action your body performs is the direct result of chemistry. A personal anecdote: The tea I’m drinking right now contains polyphenols that bind to receptors on my tongue, which I perceive as a slightly bitter yet delicious flavor (tea also has a host of antioxidants which many people know for their health benefits, but what they don’t know is that antioxidants have the special chemical property of being able to donate an electron freely, which is what causes all those great health effects (part of a phenomenon called redox reactions: more chemistry!)). The information about that flavor travels to my brain through action potentials and neurotransmitters before I ever even perceive it! What are you eating, smelling, playing, feeling, or watching that you are experiencing today through the transformative power of chemistry?