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June 2012 Archives

Disease-in-a-Dish: Converting Skin to Brain Cells

Huntington's Disease is an inherited neurodegenerative disorder that usually strikes patients in their 30s and 40s. It is a cruel disease that slowly causes mental and physical decay, manifesting in the form of dementia and loss of muscle control. Huntington's has no cure and is invariably fatal. (For those of you who were fans of the TV show House, the character Thirteen was dying from Huntington's.)

The disease is caused by a dominant mutation in a gene called HTT which encodes a protein called Huntingtin. In general, humans carry two copies of every gene, but because this disease is "dominant," only a single bad copy of the gene is sufficient to cause disease. The malformed protein which results from this mutation triggers the decay of neurons, and this causes the symptoms associated with the disease.513px-Autosomal_Dominant_Pedigree_Chart2.svg copy.jpg

Scientists researching Huntington's would like to study human cells possessing the mutation, but these can be difficult to obtain. Now, scientists at Johns Hopkins, along with an international team of researchers, have converted skin cells from healthy controls and Huntington's patients into induced pluripotent stem cells (iPSCs) and neurons.

To accomplish this, the researchers extracted fibroblasts (a connective tissue cell) from skin biopsies. They reprogrammed them to become iPSCs by infecting the fibroblasts with a genetically modified virus encoding proteins called transcription factors. Transcription factors selectively activate certain genes, and in the process, reprogram the fibroblasts to an undifferentiated state. (Though similar, iPSCs are not identical to embryonic stem cells.)

To determine if their technique worked, the researchers compared iPSCs derived from normal controls with those derived from Huntington's patients. A series of tests which examined various aspects of gene expression, cellular biology, and metabolism demonstrated that the cell lines derived from Huntington's patients behaved differently from those derived from healthy controls, and the data was consistent with previous Huntington's research. Thus, the authors successfully derived stem cell lines from the skin of patients afflicted with Huntington's disease.

Furthermore, using a cocktail of various growth factors, the authors showed that the iPSCs can be coaxed to grow into neuronal stem cells, and finally, into neurons.

Hopefully, these iPSCs and neurons will allow for faster screening of potential therapies and will expedite Huntington's disease research.

Source: The HD iPSC Consortium, Induced Pluripotent Stem Cells from Patients with Huntington's Disease Show CAG- Repeat-Expansion-Associated Phenotypes, Cell Stem Cell (2012), http://dx.doi.org/10.1016/j.stem.2012.04.027

(Diagram: An example of a family pedigree depicting the inheritance of an autosomal dominant trait. Credit: Jerome Walker/Wikimedia Commons)
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Yes, Exercise Can Help You Lose Weight

Yesterday, over at PolicyMic, Mr. Cameron English wrote an incisive article on obesity, which we linked to here on RealClearScience. In it, he implicated exercise as an ineffectual solution for weight loss.

Citing sources such as Gary Taubes, Dr. John Biffa, and Dr. Stephen Phinney, all of whom have written books touting low-carbohydrate diets as the best thing since sliced bread (though I'm not sure that they would appreciate that analogy), English lays out what seems to be a fairly convincing case as to why we shouldn't count weight loss among the benefits of exercise.

However, I strongly disagree. I believe his arguments do not properly reflect the majority of research that has been conducted on exercise in the past 50 years.

It's True that Exercise Is Not a Silver Bullet.
As a certified personal trainer, I absolutely adore exercise, but I'll be the first to admit that, by itself, it is not an incredibly effective solution for serious weight loss. Outside of The Biggest Loser, it's very difficult for an obese individual to shed pounds through exercise alone. It's far easier to eliminate excess calories from your diet (my favorite target is soda) than it is to burn them off by running on a treadmill, plain and simple.

However, Exercise Alone Can Result in Weight Loss. A 1995 meta-analysis published in the European Journal of Clinical Nutrition reviewed 28 different studies published between 1966 and 1993. The reviewers found that aerobic exercise without any dietary restriction among overweight men produced a 3 kilogram weight loss over 30 weeks compared to sedentary controls. Overweight women lost an average of 1.4 kilograms in 12 weeks. What's more, fat-free mass was not significantly effected, which means that there was little, if any, loss in muscle.

640px-US_Navy_010924-N-0063S-501_USS_Bataan_(LHD_5).jpgExercise's Effect on Appetite and Energy Intake. English repeated the distorted message that exercise makes you eat more. This is a huge oversimplification and is simply not supported by most research. In reality, exercise, especially of higher intensity, is commonly known to suppress appetite in the short term. Over longer periods, energy intake can rise without conscious regulation of diet due to increased expenditure, but this additional consumption in calories usually doesn't come close to the amount expended.   

Physical Activity's Overall Effect on Basal (Resting) Metabolic Rate is Complicated. In his article, English referenced four studies that apparently showed that endurance exercise decreases resting metabolism among overweight individuals. In truth, exercise's effect on metabolism is not that simple.

The short term effects are fairly well understood. Following a bout of strenuous exercise, an effect known as Excess Post-exercise Oxygen Consumption (EPOC) is induced. During this process, the body undergoes hormone balancing, replenishment of fuel stores, cellular repair, and muscle building, among other things. EPOC is also characterized by measurably increased oxygen intake, as its name implies. As a result of this surge in intake, your body's resting metabolism can increase as much as 13% and remain elevated for up to 48 hours post-exercise, though it will gradually taper off over that time.

The long term effects of exercise on resting metabolism are far less clear, with the results of many studies in conflict. It makes sense that if exercise results in weight loss, resting metabolism may decrease slightly simply because there is less weight to maintain. However, a habitual exercise program featuring resistance training may boost resting metabolism due to the resulting increase in lean muscle, which requires more energy to maintain than fat.

Diet & Exercise in Tandem Do Work. Though English believes "eating less and exercising more" is a "blatantly unworkable solution," there exists plenty of evidence to the contrary. A 2005 systematic review published in the International Journal of Obesity sought to examine the efficacy of diet and exercise on long-term weight loss in overweight and obese individuals. Of the 33 applicable trials found, six of them directly compared the effects of diet and exercise versus diet alone. The researchers found that diet and exercise produced 20% greater initial weight loss, and, more importantly, resulted in 20% greater sustained weight loss after one year versus diet alone.

Also, evidence for the effectiveness of eating less and exercising comes from over 10,000 individuals enrolled in the National Weight Control Registry, the largest investigation of successful, long-term weight loss. Participants in the registry have each lost an average of 66 pounds and have kept it off for over 5.5 years! 98% of registry members modified their food intake and 94% increased their physical activity to lose weight.

The Bottom Line. In the end, a lot of different methods are viable in the pursuit of a healthy weight. Exercise can work; so can simply eating less. Even the low-carbohydrate diets English embraces can work. The issue isn't finding what works. We know what works! The key is finding what works for you and sticking to it. Because the only successful strategy for weight loss and healthy living is one that can be happily maintained for life.

(Photo from the U.S. Navy)

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June 2012 Archives

Carbon Super-Materials Will Change the World

During the early 20th century there was a revolution in the materials used everywhere around us due to the inventions of polymer chemistry. Polymer molecules are long chains--only a few atoms wide but many, many atoms long--bonded covalently. (They share their outermost electrons, which is generally the strongest way atoms can bond together.)

Nylon, vinyl, polyethylene (plastic bags and sheets), mass-producible polystyrene (Styrofoam), polypropylene (plastic containers and furniture), Teflon, PVC, etc. Pretty much everything cheap that we buy and use every day was invented in a chemistry lab.

Starting in the late 20th century and taking off particularly over the past two decades, a potentially similar revolution in materials has been brewing. This time it is due to the chemical properties of carbon. Carbon is able to form extremely strong bonds with other carbon atoms.

All-carbon structures come in many forms, and three currently stand out. Sheets of carbon atoms, called graphene; hollow tubes of rolled up graphene, called nanotubes; and carbon fiber, made of stacked sheets of graphene. Each of these three extraordinary materials deserves its own story. Considered as a class, they may well similarly change what we make things out of, and, subsequently, what those things are capable of doing.

Graphene might be the best material in the world for conducting heat and electricity. A sheet of pure graphene the size of a piece of cling wrap could support a car balanced on a pencil on top of it. Right now, it is too expensive to find much commercial use, but its price has dropped enormously over the past few years and will probably continue to do so.

Carbon nanotubes, which are simply graphene sheets rolled into a tube, inherit many of the same properties. They can be used to make super-strong materials and conductors as well. Japan wants to use them to build a space elevator.

Finally, the material that is already starting to change the world is carbon fiber. It is nearly ubiquitous in applications where low weight for a certain strength is highly desirable (and worth paying for). Lance Armstrong rides entirely carbon-fiber bicycles. Major auto manufacturers are beginning to use it to build car body parts, and carbon-fiber prosthetic legs are so amazing that they may be unfair for sprinters to use in the Olympics.

CF helicopter.jpg
Cool carbon-fiber application: a human-powered helicopter the size of a basketball court. Weight? Only 75 pounds! (University of Maryland)

Beyond luxury sporting goods however, carbon fiber is beginning to become cheap enough to find other uses. Furniture, musical instruments, solar cells, scientific equipment, bridges--once the price falls low enough, nearly any structural application can be improved dramatically with carbon-fiber and other carbon materials.

June 2012 Archives

The scientific community overwhelmingly supports the use of genetically modified crops. Here is a partial list of the prominent groups in favor of GMOs:
800_gmo_crops_ap_120613.jpg
American Medical Association
National Academy of Sciences
World Health Organization (UN)
Food and Agriculture Organization (UN)
Chief Scientific Adviser to the European Commission
Department of Agriculture (US)
Food and Drug Administration (US)
Environmental Protection Agency (US)

But, apparently, an endorsement of GMOs from the world's most preeminent scientists, medical doctors, and technocrats isn't enough for some groups.

Here is a partial list of environmental organizations which are opposed to genetic modification. Note: They regularly perpetuate information which scientists have already shown to be incorrect.

Center for Food Safety
Union of Concerned Scientists
Environmental Working Group
Friends of the Earth
Sierra Club
PETA

(AP Photo)

Are Zoos Unnatural and Inherently Cruel?

Each year, over 175 million people visit zoological institutions accredited by the prestigious Association of Zoos and Aquariums (AZA), and countless other Americans visit smaller local zoos and animal shows across the country. Yet, as commonplace as a family zoo outing is in our society, many people hold underlying convictions that zoos are inherently cruel toward animals.

People for the Ethical Treatment of Animals (PETA) is a prominent trumpeter of these beliefs, arguing that zoos are "pitiful prisons."800px-Sumatran_Rhino_2.jpg

PETA and those against zoos often reach the stark, candid conclusion that animals in zoos suffer. They support this opinion by asserting a couple different things. One, that animals are inevitably confined in enclosures far smaller than their native habitats, and that this is detrimental to their health and well being. And two, that it is a breach of an animal's natural rights to take it into captivity and thus deprive it of the ability to carry out its evolutionarily established social and instinctual behaviors.

Opponents of zoos do have some evidence to back these assertions. A 2008 study discovered that elephant zoological habitats are, on average, about 1,000 times smaller than their wild habitats and that polar bears are confined in spaces around a million times smaller than their arctic territories. In addition, bottlenose dolphins in poorly-maintained dolphinariums suffer from extremely high mortality rates, and a 2002 study published in Science found that Asian elephants living in European zoos had a median lifespan less than half that of elephants living in Asian timber camps.

But for the most part, the evidence showing inherent suffering of captive animals is unconvincing. Just because one species seemingly isn't well suited to "unnatural" captivity is not evidence enough to indict all zoos. In fact, many animals, especially primates, can live much longer in captivity because they are free from predation, given medical treatment better than many Americans receive, and well-nourished. "Natural" isn't always better for an animal's health. The natural world can be a very cruel one indeed. (The video below may be disturbing to some viewers.)



In addition, most of the contentions tendered by zoo opponents fall into an anthropomorphic trap. As humans, we love to ascribe our emotional states and feelings onto other species. This is absolutely fine and endearing to do in movies like Finding Nemo or Madagascar, but it is incorrect when done in any matter involving science or policy. Biologists who study animals understand this, choosing instead to rely on strict observational evidence in their research.

"How would you like to be kept in a zoo?" is a question often emphatically yowled by zoo opponents. It's incredibly effective and tugs at the heartstrings. However, the question is a non sequitur. It assumes that humans and animals fundamentally think alike, and this is something that we still don't know for sure.

As an animal lover, I do appreciate many of the efforts championed by animal welfare groups: enforcing animal cruelty laws, promoting the ethical and humane treatment of animals, reducing natural habitat loss. But I think that their war on zoos is a misguided one because zoos actually share almost all of their goals. The only difference is that zoos go about achieving them in practical, less antagonistic ways. (PETA recently launched a porn site.)

The majority of zoos, especially those accredited by the AZA, are filled with caring animal keepers, handlers, and experts who simply love animals. Not to mention, zoos act as educational tools for the broad public, allow for the breeding and revitalization of endangered species, and permit animal research to be conducted in a controlled setting. There's nothing at all cruel about these worthy aims.

(Photo: Charles W. Hardin/Wikimedia Commons)

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June 2012 Archives

Why Are We Fascinated By Negative Space?

Negative space is commonly used in advertising and design. It is a technique where the artist creates a shape out of empty space by using the objects around it. A well-known but clever example is the FedEx logo. If you look closely, you can see an arrow made out of the empty space between the 'e' and the 'x', giving the logo a cool secondary message.

500px-FedEx_Express.svg.pngArtists also use negative space to catch the eye. On a page filled with few precious words, a patch of white sticks out like a sore thumb. The weird blankness is so out of the ordinary that we can't help but look at it.

But the idea of "negative space" doesn't only exist in visual art. It could be defined as any type of blank absence that has to be identified by the solid, constant stuff around it. When I think of negative space in this way, I find that it pops up in lot of other disciplines too.

But it seems to me that all these instances of negative space have something in common--they draw you in.

One fascinating instance I've found of this negative space idea is in film. Many movies these days seem to be haunted by a reoccurring character called the Manic Pixie Dream Girl. The MPDG has been cited in movies such as Garden State, Elizabethtown, and any movie starring Zooey Deschanel. Common characteristics of the MPDG include maddening aloofness, sickening childishness, and extreme quirkiness.

The interesting thing about the MPDG is that she isn't a real person--not even in the movies. She is only an idea that exists in the mind of the lost and tortured male protagonist. Her sole purpose in the story is to motivate the guy to get his act together, find himself, and move the plot along. Thus, without the male character, she would not exist at all.



But enough with the pop culture references. Let's cut to the chase--the idea of negative space can also be found in science.

The first scientific example that comes to mind is black holes. Everyone--especially the scientific community--is excited about black holes. And I think there's more to it than the fact that we're finding out new things about them.

Part of black holes' attractiveness has to do with their reputation for "nothingness." Now, I know that black holes are not nothing. In fact, they are pretty much the opposite of nothing because they consist of a ton of matter packed into a relatively small space. But the reason we think of them as being "nothing" is that they can't be seen using normal methods. They don't emit light, electromagnetic radiation, or x-rays that could be detected with our telescopes.

Instead, the only way to "see" black holes is by observing what they do to the objects around them. Because they are stuffed with so much matter, black holes exert a huge gravitational tug on the surrounding heavenly bodies. When nearby stars start to be dragged toward the black hole, they break apart and release x-rays, which we can then detect.

But probably the most important role of negative space is inspiring scientific discovery.

Let me explain. According to neuroscience professor Stuart Firestein, ignorance (lack of knowledge) is what propels scientists toward research. And it makes sense: scientists aren't motivated by what they already know but by what they don't know. So then if we think of ignorance as the absence, or negative space, of knowledge, it would follow that negative space fuels scientific research.

If this is the case, then negative space must be very powerful indeed.

Image: Wikimedia Commons

June 2012 Archives

Alan Turing Receives Olympic Honoring

Saturday, June 23, 2012 marks the 100th birthday of famed British computer scientist, Alan Turing. To honor his life and his incredible accomplishments, a special event will be held this weekend at the University of Reading in conjunction with the upcoming London 2012 Olympics.

"Turing100" will feature robot demonstrations, interactive machine learning programs aimed at children, and lectures on a few of the many disciplines that Turing influenced, including artificial intelligence, code-breaking, computer programming, and the philosophy of mathematics.

Alan Turing is oft considered to be the father of computer science and artificial intelligence. Among a myriad of noteworthy achievements, he invented the "Turing machine" in 1936, a device considered to be the earliest forerunner of the modern computer. He was also the first to describe in detail a stored-program computer, one capable of keeping program instructions in electronic memory. In addition, Turing developed an experiment to define machine "intelligence," called the Turing test. This was later reversed engineered into the CAPTCHA test, which you've undoubtedly taken before. It's the test that pops up when logging into certain websites meant to determine whether or not it's an internet bot or a human attempting to access protected content.

turingcaptch.jpgLeft: An artistic representation of a Turing machine. Right: An example of a modern CAPTCHA test.

Turing's Olympic honoring partially stems from the fact that he was an incredibly skilled marathon runner, posting a best time of 2 hours, 46 minutes, 3 seconds, an astounding 6 minutes, 19 second mile pace! In 1948, Turing actually tried out for the British Olympic marathon team, placing fifth in the trials.

When a friend once queried Turing about why he trained so hard, Turing replied, "I have such a stressful job that the only way I can get it out of my mind is by running hard."

Turing also suffered from other stresses that undoubtedly weighed on his mind. Chief among them, he was a homosexual in a society where homosexuality was misunderstood and actually illegal. In 1952, Turing admitted to authorities that he had a sexual relationship with another man. As a result, he was charged with gross indecency and given a choice: imprisonment or chemical castration. Turing chose the latter.

The castration, conducted via oestrogen hormone injections, left Turing impotent. He also suffered from enlargement of the breasts and a bloated physique.

Perhaps as a result of the conviction and therapy, Turing apparently committed suicide in 1954 at the age of 41. His body was discovered in his room, a half eaten apple strewn beside his bed. It is believed that the apple was laced with cyanide. Biographer David Leavitt speculated that Turing may have been re-enacting an iconic scene from Snow White, his favorite fairy tale.

Over half a century later in 2009, British Prime Minister Gordon Brown issued a full apology on behalf of the British government, saying that the way in which Turing was treated was "appalling" and that the scientist deserved recognition for his contribution to mankind.

This year, that recognition is being given. 2012 has been dubbed "The Alan Turing Year," and coordinated events are planned across the globe.

Alan_Turing_cropped.jpgA statue of Alan Turing at Bletchley Park. (Image by Jon Callas, Wikimedia Commons)

Less than a month ago, Professor Qiang Shen, Head of the Department of Computer Science at the University of Aberystwyth, carried the Olympic torch in Turing's memory.

"[Turing's] achievements led to the computerised era we live in today..." Shen said after completing his run. "Above all, his work is an inspiration to future generations of scientists and engineers."

June 2012 Archives

Public Disinterest: Our Problem as Scientists

In a thought-provoking piece published in Wired last week, writer and physicist Michael Brooks discusses public disinterest in science from the angle of mistrust of scientists.

"We are not consciously aware of it, but we have a deeply-rooted suspicion of scientists. They are not like us. They are not fun, they are not well turned-out human beings, and if pushed, we will admit we think they are dangerous."

He argues that scientists need to directly work with the general public, and children in particular, to overcome this image problem.

I agree with Brooks. As he points out, we often discourage outsiders by being withdrawn and dismissive. His argument, though, only nibbles at the edge of a bigger problem: scientists often do a simply terrible job of explaining and pitching their work and its excitement to the lay public. For every fiery Neil deGrasse Tyson there is a professor who waves laser pointers at Power Point slides or sneers at the inability of the public to grasp his work instead of trying harder to explain.

As scientists, our day to day terminology, our jargon and our common knowledge make the working language we use a code to people who haven't been trained in our fields. Even other scientists who have similar backgrounds have a hard time understanding us. Some have guessed that during technical talks, as much as 90% of the highly trained audience might be completely lost. What chance then does the general public have to understand?377px-Tycho_instrument_sextant_mounting_19.jpg

And this causes an even bigger problem: Things that we don't understand scare us.

The solution for scientists is to simplify our ideas. To take the time to picture what we are saying as it sounds to people whose technical background is different from our own. To translate from our language to theirs.

If I am speaking to another physicist who specializes in quantum optics measurements, I might describe a complex piece of scientific equipment (a spectrometer) in very technical terms. I'll invoke increasingly inscrutable qualities: lines per millimeter, spectral resolution, spatial dispersion and, scariest of all, quantum efficiency.

My words must change completely when I describe it to a seventh grader or a high school teacher. I rely on analogies to everyday objects, perhaps a prism or a rainbow. I try to compare it to something that is cool. The camera inside is like an iPhone camera, but one million times better. I can describe how many thousands of colors there are and how the machine can see how much of every single one there is. Maybe I will pour out some liquid nitrogen that is used to cool the machine just because it is fascinating to watch.

This translation work consumes time and energy and some who love technical work may not enjoy it.

But, to bridge the gap between our own enthusiasm for our science and the enthusiasm of the general public, we must take this responsibility upon ourselves. John Q. and Angie M. Smith have no obligation to give their tax dollars to us or care about what our research means for their lives. We have to go out and sell our work to them and their children.

We need science communicators every bit as much as we need professional researchers. By mobilizing the public, we may ultimately achieve as much as we would by investing our time in research itself!

(Image: Wikimedia Commons)
Science has a sense of humor, and I've got the videos to prove it. Allow me to count down five of my favorites:

5. It's Not Y.M.C.A., It's G.T.C.A. Sure, the majority of scientists can't dance or follow choreography even if their their lives depended on it, but they can craft a pretty awesome lyrical parody. This one seamlessly supplants Village People's "Y.M.C.A." with "G.T.C.A." -- Guanine, Thymine, Cytosine, and Adenine, of course.
 



4. Ask Mr. Lizard. What do you think would happen if you mixed potassium nitrate, charcoal, sulfur, and muppet dinosaurs? Find out on "Ask Mr. Lizard!"




3. Imitating a Nuclear Explosion. Steven Colbert wanted to convince Joseph Cirincione of the Ploughshares Fund  -- a group with the goal of nuclear disarmament -- that a nuclear explosion is totally awesome. What better way to do that than to engage in a little wild gesticulation meant to emulate the denotation of a nuclear bomb?




2. Robot Stand-up Comedy. Robots build cars, vacuum floors, play soccer, fight wars, and now perform live stand-up comedy. Check out Heather Knight's robot, Data, on-stage at TEDWomen 2010.




1. A Drunk MythBuster Gets on a Treadmill... The pursuit of scientific knowledge occasionally requires stressful, even painful exertions, working overnight in laboratory, navigating a hot, humid in insect-ridden jungle, or running on a treadmill drunk, for example. In an episode of MythBusters, Jamie Hyeneman and Adam Savage wanted to find out if vigorous exercise works as an effective sober-up technique. Savage was the unlucky guinea pig for this one. Watch what happens when he jumps on the unforgiving, fast-moving belt of a treadmill... after taking six shots of liquor.

June 2012 Archives

Vaccine Debate Drives Married Couple to Divorce

In 2008, a British Columbian couple split up after three years of marriage. Uniquely, the primary driver of their feuding wasn't money or infidelity; it was a fundamental disagreement over whether or not to immunize their young son. As CTV News reports:

The boy's mother suffered from seizures and high fevers after she was immunized as a child, and she also shares a commonly held but repeatedly debunked belief that vaccines can cause autism. Her estranged husband, on the other hand, was convinced that the boy should receive all immunizations recommended by the provincial government.
The split couple recently made their separation official in divorce court. As part of the proceedings, both sides argued for the power to decide the vaccination fate of their son. Now five years old, the boy has yet to receive any immunizations.
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To support his side of the case, the pro-vaccine father enlisted the aid of immunization expert and pediatrician Dr. David Scheifele. In a written report to the court, Scheifele debunked the mother's alarmist and pseudo-scientific positions and also spoke further on the notion of herd immunity and how failing to vaccinate the child could potentially put others at risk.

"If overall vaccination rates slip, infections previously held at bay can return to cause outbreaks among susceptible children and adults. Given that childhood vaccination rates in B.C. are suboptimal ... one can predict that periodic outbreaks of some vaccine-preventable infections will occur and could involve [this child]," Scheifele said.
Justice Catherine Wedge decided to grant the divorced parents equal power in decision-making over their son's welfare, except on the matter of vaccinations. On this, she granted full authority to the father.

Now, this case wasn't exactly as consequential as a Supreme Court case, but it's good to see that science, not pseudo-science, still holds sway in the court system. The same cannot always be said when it comes to politics or the general population.

(Photo by Nati Harnik, Associated Press)

June 2012 Archives

Thanks, Dad! You've Been Like an Emperor Penguin.

Newton Blog presents an open letter to dads everywhere...

Well, dad, your day is fast approaching. This Sunday, sit down on a sofa, kick up your feet, grab a Sudoku, and relax. You earned it.

But before you do that, I'd like to take some time to say, "Thank you." Fatherhood is no easy task; there have been some bumps along the way. But overall, you've done a wonderful job.

Numerous surveys and studies have suggested that your love was critical to my early development, perhaps even more so than mom's. Because you were involved, nurturing, and playful when I was a baby, I had better linguistic and cognitive abilities as an adolescent, and even a higher IQ! Though it didn't always seem like it, I was also more confident to explore my surroundings and more emotionally secure. (Yes, dad, I know those are just correlations, but I'm still giving you the credit!)

An experience that was undoubtedly beneficial for me has been, at times, somewhat of a mixed bag for you. You've had to give up a lot of your time, energy, and resources, all to take care of squalling, messy, demanding, young me. Not to mention, your testosterone levels have dropped precipitously, no doubt leaving you feeling a tad less masculine.

But hey, it could be worse! You should be happy you aren't a male orb web spider father. When he mates, he detaches his "sex organ" and leaves it fastened to the female. And almost 75% of the time, he gets eaten by his much larger lover!373px-Aptenodytes_forsteri_-Snow_Hill_Island,_Antarctica_-adults_and_juvenilnewtone-8.jpg

Fatherhood also has had some advantages for you. David DeGarmo, a research scientist at the Oregon Social Learning Center just told the USA Today that fatherhood offers "mental health, well-being and actual physical health benefits."

In addition, Richard Settersten Jr., professor of human development and family sciences at Oregon State University conducted a study showing that "fatherhood prompts men to be less self-centered, more giving and more outward-focused."

Overall you haven't been a deadbeat like a lion, lounging around all day, occasionally roaring, and making mom do all the work. No, you're more like an emperor penguin: watchful and caring, a constant in my life.

Thank you for being there, and Happy Father's Day!

(Photo: Animal Portraits/Wikimedia Commons)

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June 2012 Archives

Lethal Injection Protocol Needs Science

On Tuesday, Idaho became the second state to use a new type and method of lethal injection.

Traditionally, lethal injection is administered using a three-drug cocktail that sequentially sedates, paralyzes the muscles, and stops the heart. The problem is, this drug "cocktail" isn't really a cocktail because the components can't be mixed together. Instead, each drug is administered sequentially with a separate injection.

The idea is that each of the three drugs should be administered in lethal doses so that the procedure is redundant. However, a study published in 2007 brought into question whether this is actually the case.

After analyzing execution records from North Carolina and California, Zimmers et al showed the three-drug method may not be effective due to a lack of sedative used in the procedure or a poor injection technique. In fact, the study showed that in some cases, not only is the sedative dose not lethal, but it also may not actually sedate the inmate entirely. Without the sedative, the inmate would be in serious pain from the other drugs. But the pain wouldn't be apparent because the second paralyzing drug would keep the inmate from expressing it.

One possible alternative to the three-drug protocol is a single-drug protocol, consisting solely of a larger dose of the sedative. However, this method has its drawbacks too. While death occurs about 10 minutes after injection with the three-drug method, the single drug method can take up to 45 minutes. This one-drug method was first used in Ohio in March of 2011 and has been used by several states since.

But the injection method wasn't the only unique aspect of Tuesday's Idaho execution--the type of drug used for the sedative was also unique.

In the past, the preferred sedative for lethal injection was thiopental, a fast-acting drug often used in hospital procedures. However, in January of 2011 the only U.S. company that manufactured thiopental announced that it would no longer be selling it. This decision came about directly because the of the drug's use in lethal injection. European companies also won't sell the thiopental to the U.S. for use in lethal injection.

States turned to a different sedative, phenobarbital, which is in the same family as thiopental. Since then, phenobarbital has often been substituted for thiopental in the three-drug protocol and also in the one-drug protocol, like the the Idaho case.

Now phenobarbital stock is also running low. As with thiopental, there are no American manufacturers, and Europe will not sell it to the U.S. for use in lethal injection.

But the issue isn't that we need another sedative. The issue is that scientific professionals have not been consulted to evaluating lethal injection procedures. Zimmers summed up the problem nicely in an interview with Scientific American.

There's no record of a medical or scientific inquiry into whether this would be the best method. And there isn't any medical evidence to support this approach. Part of the paradox is that it looks like a medical procedure, but it hasn't been rigorously tested. There are no controlled trials, data collection, analysis or peer review of the processes to determine whether it works the way it's been said to work.

Since Zimmers and her team published their study, the lethal injection protocol has changed with the switch to phentobarbital and the one-drug protocol. Despite these changes, still no peer-reviewed protocol has been established.

(Image from the Associated Press)

June 2012 Archives

These Animals Lived Longer than You

The life expectancy of the average American is not too shabby. 78.5 years is plenty of time to learn plenty, love lots, and live a pretty darn good life. But 78.5 years pales in comparison to the ages achieved by some of our bestial brethren:

Henry the Tuatara. Tuataras are small lizard-like reptiles endemic to New Zealand, and at 113 years old, Henry is one of the oldest known.  Despite his comparatively senescent age, Harry's handlers at the Southland Museum in New Zealand believe that the centenarian could easily live to be a bi-centenarian.

Harry's long life expectancy, coupled with the fact that he apparently sported a hidden tumor on his genitals for an unknown duration, may explain why he waited 110 years to mate for the first time! And you thought being a 40-Year-Old Virgin was embarrassing...

Henry_the_tuatara.jpgLookin' good, Henry! (AP Photo)

The Bowhead Whale. In 2001, whale biologist Craig George made an interesting find examining the corpse of a bowhead whale. He discovered a century-old harpoon point buried within the cetacean's blubber. This was one old whale!

That specimen turned out to be between 110 and 115 years old, but it didn't even come close to a bowhead that George had previously discovered. In 2000, George sent 48 frozen bowhead eyeballs that he had collected over two decades to Jeffrey Bada of the Scripps Institution of Oceanography. By analyzing changes in aspartic acid within the samples, Bada calculated that the oldest whale was 211 years old at the time of its demise, which made it the longest living mammal known to science, a record that has not been broken to this date!

800px-Grönlandwal_3-1999.jpgA bowhead whale. (Angsar Walk, Wikimedia Commons)

Happy & Healthy as a Quahog Clam. Believe it or not, sclerochronologists can determine the age of a clam very similarly to the manner in which dendrologists calculate the age of trees. They simply count the number of annual growth lines.

In 2007, scientists from Bangor University discovered a quahog clam off the coast of Iceland with approximately 400 of these lines! A detailed assessment later proved what the researchers had already excitedly surmised: the clam was over 400 years old!

Multi-century-old clams are actually nothing new. Scientists theorize that the mollusks "may have evolved exceptionally effective defenses which hold back the destructive aging processes that normally occur." Their astounding longevity may also have something to with the fact that they live a comparatively "shelltered" life.  

1.jpgImage from Bangor University

June 2012 Archives

Black Hole Hunting

While actively fighting in the German army in the trenches of the Russian front in 1915, Karl Schwarzchild wrote Albert Einstein a letter. The letter contained the first known solutions to Einstein's brand new equations of general relativity. (Schwarzchild was to tragically die months later, only 42, of an illness contracted during the fighting.) Largely unexplored at the time was the fact that these solutions allowed for the existence of a singularity in spacetime, that is, a place where curved spacetime disappears into an infinitely deep hole which matter and light cannot flea fast enough to escape (with one exception).

Another brilliant man, Subrahmanyan Chandrasekhar, performed his own calculations under interesting conditions (a voyage from his home country of India to England). He showed that white dwarf stars with a large enough mass cannot survive, and will be crushed by their own gravity. While some of these stars can become other strange objects such as neutron stars, most are destined to collapse into singularities. These came to be known as black holes.

The NuSTAR telescope, being launched today by NASA expects to detect far more of these objects than we have ever seen before, and to study their properties in much finer detail.

As outside observers, how can we find a black hole? It's surface is frozen in time and once it comes too close, nothing escapes it's clutches for us to see. So what is there to look for? The answer is that we can watch the effects of their consumption of other stars. Very often in the universe, two stars orbit each other, in what is known as a binary star system. When one of these stars becomes a black hole, the two continue their orbit as before, but gradually small bits of the non-black hole star can come too close to the black hole and begin to fall into it. This matter gives off very bright X-rays as it is being sucked in.

In this way the black hole swells and its increased mass pulls the other star in closer, eating more and more of the unfortunate companion. The dying matter shoots out X-rays into space, which we can see and identify as coming from such an event. 

Black Hole Accretion.png
A star being devoured by its companion black hole (artist's conception, NASA)

Earth's atmosphere absorbs X-rays however, making observation from the ground difficult. This necessitates using a space telescope.

The Chandra X-ray telescope (named after Chandrasekhar), launched in 1999, has already found many many black holes. NuSTAR however will be able to see a broader range of different X-rays (more wavelengths). More importantly, it's design is much improved. The new telescope will expand out to 10 meters (33 feet) in length and will use X-ray optics to detect signals 10 to 100 times better than the previous telescope.

NuSTAR joins a distinguished collection of other telescopes (Hubble, Spitzer, Chandra) orbiting the planet. All of these instruments have drastically expanded our view of the universe.


June 2012 Archives

On May 24th, Temple Grandin, the heralded animal scientist responsible for revolutionizing the livestock industry, weighed in on the recent "pink slime" controversy. Speaking with Tim Carman of The Washington Post's All We Can Eat Blog, she came out in "clear support" of Lean Finely Textured Beef (LFTB) -- "pink slime."

"It should be on the market. It should be labeled. We should not be throwing away that much beef," Grandin told All We Can Eat.

Carman went on to further detail the wisdom behind her rational stance:

By Grandin's calculations, cattle producers will lose about 15 to 30 pounds of meat per animal without the filler. "That's sinful," she says. For big plants, it's like taking a "truckload of cattle and [saying], 'We're just going to throw these cattle into the garbage.' "
But wait, you might be thinking, that whole pink slime commotion was like two months ago... What the heck took her so long to say something?

The answer, my friends, is backstopped by two attributes often lacking in our public discourse: Temple Grandin used logic and reason.

Grandin modestly admitted that when the controversy broke out back in March she didn't actually know very much about LFTB. Thus, she sagaciously decided to stay mum on the subject.

"I only like to talk about things that I know about," Grandin told All We Can Eat.

Only after thoroughly educating herself on the topic so that she could form a cogent conclusion, did Grandin finally offer her opinion on the subject. What a novel concept!

If the alarmists that fueled the original uproar had followed Dr. Grandin's example, they likely would have have learned a lot of interesting things about LFTB:

  • "Lean finely textured beef has been in our food supply for 20 years without one case of reported illness."
  • Ammonium hydroxide, the chemical used to treat lean finely textured beef, is recognized as safe by the USDA.
  • A tofu burger contains four times the amount of ammonium hydroxide as a hamburger using lean finely textured beef.
  • A recent study has shown that lean finely textured beef can improve color, reduce spoilage, and increase tenderness of ground beef, all while reducing the average cost by 20 to 25 cents per pound.
  • From a "microbial-pathogen view," lean finely textured beef actually has a better safety record than normal ground beef.
  • Though lean finely textured beef is often called "pink slime," it is nothing like the pink slime that came out of Sigourney Weaver's bathtub faucet and tried to eat her in Ghostbusters II.

Corndog_Inside.jpg
Embrace the slime. (Source: Stezton/Wikimedia Commons)

Perhaps, if the public had been aware of these facts, the masses may have not been so hasty to decry and vilify LFTB, and 650 workers at Beef Products, Inc. -- the manufacturer of LFTB -- might still have their jobs.

Follow me on Twitter @SteRoPo

June 2012 Archives

My Six Years in Graduate School

In my previous life as a research scientist, I spent 10 years studying microbiology. As an undergraduate, I majored in microbiology (with a chemistry minor), and as a graduate student, I spent six years getting a Ph.D. in microbiology. After that, I joined the team at RealClear. Inevitably, whenever I tell people this story, they ask, "So... what did you study in grad school?"

My doctoral dissertation (which you can find here) examined how structural changes in a bacterial membrane molecule influence the human immune response. Specifically, I examined a bacterial molecule called "lipid A," which is found only in the outer membrane of Gram-negative bacteria. (FYI, Gram-positive bacteria have one membrane, and Gram-negative bacteria have two -- an inner and an outer membrane.)

800px-Gram_negative_cell_wall.svg.pngGram-negative bacterial cell wall. (Source: Jeff Dahl/Wikimedia Commons)

The lipid A molecule is medically relevant. The best-known version of the molecule is the one produced by E. coli, and it is the most immunologically active lipid A known. The E. coli lipid A (and other lipid A molecules with a similar structure) strongly activates the human immune response. This particular immune response, known as inflammation, is normally a good thing. It helps clear our bodies of pathogenic bacteria. But, taken too far, inflammation can be deadly. That's why blood infections are so serious. Bacteria circulating in the bloodstream can trigger systemic inflammation, which can cause leaky blood vessels, a dramatic drop in blood pressure, multiple organ failure, and death.

456px-Lipid_A.png
Structure of E. coli lipid A. (Source: Edgar181/Wikimedia Commons)

However, not all lipid A molecules are created equal. Some are much more immunologically active than others. Look at the E. coli lipid A structure above. See those long, dangly-looking things? Those are fatty acids. E. coli lipid A has six of them. Also, in the upper-left and upper-right corners of the molecule, you should see a "P" (which stands for phosphorus) surrounded by oxygen atoms. Those are phosphate residues. E. coli lipid A has two of them. Deviations from this structure usually result in a much less potent lipid A. That's where my project comes in.

I was investigating the lipid A molecules produced by Bacteroides fragilis (a backstabbing, two-faced gut bacterium that is sometimes friendly and sometimes evil), Bacteroides thetaiotaomicron (a much friendlier gut bacterium), and the evolutionarily related Porphyromonas gingivalis (the bacterium associated with periodontitis, i.e., severe gum inflammation which can lead to tooth loss.) All three bacteria produce a lipid A molecule with only five fatty acids ("dangly things") and one phosphate group, instead of two. All three lipid A molecules are much less potent than that of E. coli, but they are not equal in potency.

In my first paper, we discovered that both species of Bacteroides produce a lipid A molecule that is much more immunologically active than the one produced by Porphyromonas. In my second paper, we figured out why: Bacteroides produces lipid A with a single phosphate group in the upper-right corner of the molecule, while Porphyromonas produces a lipid A with a single phosphate group in the upper-left corner of the molecule. That small difference was responsible for the enormous disparity in immunological potency between the lipid A molecules.

What are the applications of our work? First, understanding the basic microbiology of how bacterial molecules can make us sick is important in and of itself. And second, understanding how lipid A structures activate the immune response could prove useful in designing more effective adjuvants, which are important in producing good vaccines.
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June 2012 Archives

256px-Rooster_portrait2.jpgThis month, Smithsonian published a fascinating article about the history of chickens and how they basically took over the world.  Obviously, chickens couldn't have established their empire without reproduction, so I thought I'd take a behind-the-scenes look at how chickens became so prominent.

As it turns out, chicken procreation is a lot weirder than I thought. Here are just a few of the finer points.

1) Asymmetrical gonads


Here's how gonads are usually arranged: males have two testes, and females have two ovaries. Both genders usually have one gonad on the right side of their body and one on the left. It's pretty simple.

In contrast, hens only have one functional ovary. In fact, most birds have this lopsided anatomy probably because it's more practical for flight. Birds need to be light and compact in order to fly, so they only develop one of their gonads.

For most male birds, the right testes is also smaller than the left. This trend does not carry over into roosters, however, probably because chickens are land-dwelling birds. In some bird species, the smaller right testes can even compensate if (God forbid) the left one gets damaged.

2) No copulatory organs

As with most bird species, roosters and hens don't have external genitalia. Instead both partners procreate using an external orifice called a cloaca. When the cloacae are touched together, sperm is transferred into the female reproductive tract. Since no penetration is involved, the act is simply called a "cloacal kiss."

Both genders also use their cloacae for defecation. But don't worry--chicken eggs do not get covered with feces on their way out. When a hen lays an egg, her uterus turns inside out beyond the cloaca that the egg never touches the nasty stuff.

3) Most are virgins

After a rooster inseminates a hen, her eggs will be fertilized for up to four weeks. This is because the sperm remains viable for about 30 days, stored in "sperm nests" along the hen's oviduct.

However, hens don't actually need need roosters in order to lay eggs. In fact, most hens raised in commercial farms have never even set eyes on a rooster.

The only thing hens need in order to stimulate egg-laying is light. Hens are programmed to lay eggs in the spring and summer, which they judge by the amount of daylight. Of course, commercial farmers tap into this tendency by simulating summer days in their chicken coops all year around.

4) Very productive

Chickens are egg-laying machines. A hen hits puberty only 18-24 weeks after hatching out of an egg herself. It only takes about 26 hours for a hen to make an egg, and she can start producing another one 40-60 minutes later. What's more, hens lay a lot eggs--up to 300 a year.

Comparatively, turkeys, are lazy slobs. They start laying eggs later than chickens and lay 100 eggs a year at the most. Because of these and other factors, turkey eggs are a lot harder to come by than chicken eggs. One farmer valued a turkey egg at $3.50 per egg. So that's why we don't use them for omelets.

5) Unique egg shell pigment

So get this: out of the 26 hours it takes to make a chicken egg, 20 of those hours are required to make the shell. Which I guess shows you it's pretty important. Probably the most aesthetically important step of making the shell--adding the pigment--occurs in the last few hours of shell formation.

Egg color is useful because it's is an expression of the bird's fitness. It also makes them look pretty. It seems that this quality is especially important to private chicken farmers.

Differing types of pigment make some eggs a lovely brown or a mysterious blue. The pigment that makes blue eggs is called biliverdin, which is a precursor to the bilirubin pigment that is found in blood. After some dispute, one study showed that biliverdin doesn't come directly from the chicken's blood. Instead, it is produced separately in the chicken's uterus.

Interestingly, recent studies have shown that the enzyme that converts biliverdin to bilirubin in humans is an important regulator of the innate immune response.   

6) Can't be twins

Chicken "twins" occur when the ovary releases two yolks at the same time. The yolks are processed together down the chicken's oviduct and a single shell forms around them. Thus two chicken embryos are encapsulated by the same egg.

Once the chicks are ready to hatch, they encounter a problem. In order to get out of their egg, they have the peck at an air space at the top of their egg. But there is simply not enough room for both of them to crane their heads around and peck, so they fight each other instead.

Usually, both twins end up dying--unless they are rescued by a chicken "C-section" performed by a skilled human.

Photo by Muhammad Mahdi Karim via Wikimedia Commons

June 2012 Archives

A Burning Need for Better Science Communication

What is a flame? It's a simple enough question. One you'd think would beget an equally simple and comprehensible answer. But no, for such an elemental phenomenon, one so essential to mankind's success as a species, flame is as mystifying to most as it is mesmerizing.

This is especially true among children, boys predominantly, who I think all suffer from a mild case of pyromania at one time or another. I know I did, and it appears that Alan Alda, the famed television actor from M*A*S*H, did so as well.

As an inquisitive sixth-grader, Alda was transfixed by the searing, fluttering, blue, yellow, and orange-ish entity alighting the wick of a candle, so he asked his chemistry teacher about it.

"What is a flame?" he queried.

"It's oxidation," she answered.

Years later, Alda, now a board member at the Center for Communicating Science, recalls being dispirited by his teacher's response.

"I knew there had to be more to the mystery of a flame than just giving the mystery another name," Alda wrote in a guest editorial appearing in the journal Science.

To Alda, the situation perfectly exemplified what's wrong with the way science is commonly communicated. When speaking with the general public about perplexing topics, scientists often explain their craft in a manner twice as bewildering as whatever provoked the original question. This is not purely the fault of scientists. There's simply a massive disconnect between them and the general public. How the two groups think, speak, and act can be vastly different.

Luckily, it doesn't have to be this way. The rift can be remedied. To accomplish this noble end, Alda helped found The Center for Communicating Science at Stony Brook University in 2009 and, more recently, concocted "The Flame Challenge" based on his prior experience asking about flame in grade school. The challenge's goal? To explain science to an eleven-year-old in a manner that is both understandable and educational.

The winner of "The Flame Challenge" was just announced this past Saturday, and the prize went to Ben Ames, an American working towards his PhD in quantum optics at the University of Innsbruck in Austria. He masterfully explained a flame in a playful and colorful seven-minute animated video.

Narrating the video himself, Ames' adopted a tone that was childlike, but not overly simplistic. And he didn't shy away from using complex terminology, adeptly weaving the scientific intricacies into his video by walking the viewer step-by-step through the makings of a flame, building upon prior teachings at each new stage, and constantly offering reminders to cement it all together.

What is a Flame from Ben Ames on Vimeo.


Of course, "The Flame Challenge" was only a playful attention-getter for a broader effort to improve science communication to the general public, the importance of which cannot be overstated. A skilled physics, chemistry, or biology teacher can transform a daunting subject into one that's easily understood, thus encouraging students to eagerly press forward in learning, instead of dejectedly dismissing their studies as "too hard" or "above them." A researcher can ensure that the public understands the scientific complexities of pressing issues within their field. Thus, an engaged public can partake in sound decision-making based on factual evidence instead of potentially baseless ideology.

Communicating science in a way understandable to the average individual is no easy task. But it's a challenge well worth undertaking.

June 2012 Archives

Internet Deprivation is No Laughing Matter

Think Internet deprivation isn't serious?  Think again.

I once heard tell of a terrible case. The poor girl who was afflicted didn't know what hit her until it was all over. She was only 21... so young.

It started innocently enough. Facebook wouldn't load. Nor would Wikipedia or Perezhilton. She tried unplugging the router and plugging it back in. It didn't fix the problem. What was there to do but wait it out?

She plopped herself down belly-first on the living room couch and turned her head to face the 50" plasma television. Grudgingly, she snatched up the remote from the bowels of the sofa. The click of its buttons wasn't nearly as satisfying as the click of a wireless mouse. Advertisements plagued almost every channel, like pop-ups that couldn't be blocked. After mere minutes she was fed up and could take no more.

Desperate for stimulation, the girl made a drastic decision: she picked up a book. It was an interesting read, something about vampires. But after five minutes the subject matter grew dull; it was unchanging, stagnant, and required an attention span. She longed for variety, for news, to comment on an Instagram photo, or to click on a link that might give rise to an amusing adventure. Reading firmly printed words on bound pieces of paper would not, could not, sate these burning desires.

Insanity took hold thereafter. The internet-deprived girl slowly withered into a dithering, blithering blob, her brain not much more than gelatinous goop.

The Internet had been off for only twenty minutes.


4670882c-b304-4e3d-948b-e9815240a5c8.jpgThe effects of internet deprivation aren't quite this pronounced, but they are very real. In a first-of-its-kind experiment, consumer researchers with Yahoo! and advertiser OMD recruited 28 participants from thirteen households and deprived them of Internet for fourteen days. Subjects reported succumbing to "withdrawal and feelings of loss, frustration and disconnectedness." Mind you, this was in 2004... before Facebook, before Twitter, before YouTube!

More recent studies examining Internet deprivation have shown similar results. In 2008, British psychologists studied heavy internet users in a clinical setting and found that their brain activity and blood pressure increased markedly when they were disconnected. They creatively termed this phenomenon, "discomgoogolation."

In 2011, two different surveys each asked 1,000 participants to abstain from using the Internet for at least 24 hours. Both similarly found that the majority of Internet-deprived participants felt dependent on the technology. In one of the surveys, British consumer research firm Intersperience discovered that 53% of participants reported feeling upset and 40% reported feeling lonely. Many described the experimental ordeal as a "nightmare."

Whether or not Internet addiction is a genuine condition is a topic actively debated by psychologists, but a solid case can certainly be made that Internet deprivation has become, or is evolving into, a form of social deprivation. Over 2.3 billion people currently use the Internet, that's 30.2% of the world's population. In the United States, the percentage is 79.3%. With so much social interaction being performed in forums, via social media, on news websites, or via email, you have to ask, can a person deprived of the Internet in this day and age be successful in life or even develop normally?

I'm not sure that they could.

(Photo by the Associated Press)

Footnote: This story was inspired by fellow Newton Blogger Katherine Dickinson, who suffered through a harrowing bout of internet deprivation two weeks ago and barely escaped with her sanity intact.

June 2012 Archives

Venus: Near-Earthly Body

Yesterday the world watched as the planet Venus "transited" our sun. Millions of people squinted into capped telescopes and home-made pinhole cameras. In a display that shocked the physicists working in my department, so many local people came out to see viewings put on by the astronomers down the hall that they filled a 14 story staircase and several floors of office space. What is so interesting about Venus, and what can scientists learn from this event?

Venus is of particular interest to scientists foremost because of its similarity to earth. Like our planet, Venus sits at a comfortable distance from the sun (it is our closest neighbor most of the time). It too has an atmosphere with nitrogen and carbon dioxide. The upper layers of its atmosphere are very similar in composition and pressure to earth. Thick clouds and ozone swirl there, lightning crashes down on the surface and volcanoes erupt because of tectonic activity. Venus is roughly the same size as earth and is composed of many of the same elements.

Despite these similarities, one way to describe Venus is "like earth, gone to hell!" If you tried to stand on the surface, pressure similar to that roughly 3000 feet (~915 meters) underwater would crush you instantly. The surface temperature of nearly 900 degrees F (~480 degrees C) would combust you almost as quickly. Clouds of extremely caustic sulfuric acid drift through the air. Russia sent a series of probes to Venus and none of them lasted more than 110 minutes before being eaten by these extreme conditions.

What created this brutal atmosphere out of constituents similar to those on our planet? One possible answer: greenhouse effects. This could give us a chance to observe the effects of this process, which  is potentially threatening our own planet, in its extreme stages.

The transit event also gave us an exceptional (and rare, this is only the sixth occurrence since Newton was born; it won't happen again until every person alive now is well over 100 years old) chance to study the planet's atmosphere as well as planets in general. In 1639 one of these transits was used to make the first measurement of the size of the solar system. This was a huge leap for astronomy at the time. During this transit, astronomers looked mostly at two things.

First, they observed the planet in profile: that is to say it was positioned perfectly such that the huge light source of the sun sat behind it and the surface features of the planet stood out blocking the light. This is like holding a small object up to the light and squinting at its edges to see it better. Scientists can investigate particular shapes and formations of gas and clouds to try to learn more about particular weather patterns of the planet. 

655868main_venus-arc SM.png
The Venus "arc": a mystery related to the atmospheric composition of Venus (NASA)

Scientists also plan to use data gathered about this passage to help us in our continued search for exoplanets. We often detect exoplanets by seeing them pass in front of the stars they orbit. Our close-up observations of this process will help us better understand it when we see it far, far away.



June 2012 Archives

Things to Do with Soda... Besides Drinking It

400px-Diet_Coke_Mentos.jpgYou may disagree with New York mayor Michael Bloomberg on how to handle the "problem" of carbonated sugar water, but he is right about one thing: soda is not good for you.

In fact, it's the number one source of added sugar in the diet of American children and may be the single greatest dietary contributor to weight gain and overall poor health for individuals.

To the scientists studying the growing obesity epidemic, this much has become clear. Their recommendation? Cut down on soda consumption, and if possible, remove it from your diet altogether.

But this begets an an inconvenient problem. If thousands of Americans drop drinking pop like the bad habit it is, what will they do with the built-up stockpiles of soda in their homes?

Luckily, there are a few amusing soda science experiments that anyone can perform in the comfort of their own home. These can serve as a semi-productive way to use up that leftover soda.

Sinking Sunkist Surprise. This is a great one for the kids, and it's very simple. All you have to do is fill up your sink with water and grab two cans of soda -- one diet and one regular -- preferably of the same variety. Gather an audience and slip the normal can into the water. It sinks. After providing a bit of dramatic build-up, drop the diet can into the water. It floats! What the Dew (Mountain, of course) is going on here?

The answer is that the two cans have different masses, and thus different densities. The normal soda contains as much as 40-plus grams of sugar, while the diet soda contains none.

Root Beer Balloon. Another easy one. You'll need a bottle of soda and a balloon. Simply open the bottle and firmly fix the balloon over the top so that no air can escape. Over time, the carbon dioxide will slowly escape from the liquid and inflate the balloon!

Corrosive Coca Cola.
How many times have you been badgered by your dentist to drink less soda? Chances are, a fair amount. The logic behind this persistent nagging stems from the fact that soda is incredibly acidic, with a pH sometimes as low as two. And exposing your teeth to highly acidic substances for prolonged periods can corrode their enamel.

To accentuate and demonstrate this fact, gather a variety of different sodas, one plastic cup for each type, and one tarnished penny for each type. Place a penny in each cup and pour different sodas over them. Over the following hours and days, watch as the soda dissolves extraneous substances and removes corrosion on the pennies. You'll notice that some sodas will perform better than others. This is because they are more acidic!

Diet Coke and Mentos. This is perhaps the granddaddy of all soda experiments and the best way to quickly use up your supply. For this, snatch up some regular Mentos and liberate that forgotten, unopened two-liter of Diet Coke from the recessed innards of the fridge. Then, take both of these materials outside onto the grass or road and open the Diet Coke. When ready, drop any number of Mentos (the more, the more explosive) into the bottle and quickly stand back and watch as foamy brown sugar water erupts from the bottle.

Newton turns to the Mythbusters to explain this soda volcano:

Look at a Mentos close up and it's like the surface of the Moon and that might be the candy key. Drop one in cola and every tiny crater provides a site where a carbon dioxide molecule can change to gas. Because Mentos are so pitted, the theory is that carbon dioxide bubbles are formed in a very short space of time and because this candy sinks and because this rapid release of gas happens at the bottom of the cola, you get that famous fountain.

(Image by Michael Murphy from Wikimedia Commons.)

June 2012 Archives

Have Emoticons Improved Written Communication?

It was September 19th, 1982 when written communication changed forever. On that fateful day, Scott Fahlman, a research professor of computer science at Carnegie Melon University, strung together three punctuation marks -- a colon, a hyphen, and a parenthesis -- for the very first time. The skies opened and light shined down as the trio of marks melded together into an image unmistakable to any human onlooker, provided that they cocked their head to the left.

Binette-typo.pngThe smiley was born, and with it, emoticons.

It took many years and many technological advancements before emoticons would gain total ubiquity. Today, they pervade almost all forms of written, computerized communication, be it texting, chatting, or emailing. The business community held out for a good while, clinging to a dogma of strict professionalism. But now, suited businessmen and women across the world are succumbing to the use of ;-), 0.0, and <(^_^<) <(^_^)> (>^_^)>.

Of course, not everyone is happy about emoticons overtaking written words.

"I am deeply offended by them," Maria McErlane, a British journalist, actress and radio personality on BBC Radio 2 told the New York Times. "I find [emoticons] lazy. Are your words not enough? To use a little picture with sunglasses on it to let you know how you're feeling is beyond ridiculous."

And she isn't the only one. Again from the New York Times:

'Once upon a time, people could communicate emotions effectively simply through the tone of their writing,'' wrote a Slashdot reader under the name KnifeEdge. ''Now that people have apparently lost this ability, they use a crude text representation of a facial expression. This is not an improvement.'.

Personally, I agree with these opinions. Emoticons have not improved the collective coherency with which we write. The emotion and eloquence that was once conveyed by skillful use of proper punctuation and descriptive adjectives have been lost, replaced by frownies, winkies, and smilies.

Though I firmly believe that emoticons are robbing us of our written abilities, there is no doubt that they have proven useful in online communication. For example, a smiley or a winky makes it much easier to relay humor or sarcasm without worrying that your delightfully dry wit will be misconstrued. Emoticons add a nonverbal element to written communication, which makes it much easier to effectively communicate with others. John Sener, an educator with over thirty years of experience and a pioneer of online learning, actively recommends that his students use emoticons in online learning environments such as forums or chat room discussions. He even provides his pupils with training on how to properly use them.

The notion that emoticons facilitate written communication also has some backing from scientific studies. In 2010, researchers from Tokyo Denki University used functional magnetic resonance imaging to analyze brain activity in subjects viewing emoticons attached to a sentence. They discovered that seeing an emoticon activates the left and right sections of the inferior frontal gyrus, areas of the brain associated with verbal and nonverbal communication. The left inferior frontal gyrus is also known to be extremely important for language production and verb comprehension.

Another study, conducted in 2008 by scientists at Open University of the Netherlands, investigated the role of emoticons in "computer-mediated communication," doing so via a questionnaire and by conducting experimental internet chats. The researchers found that participants used emoticons in an attempt to mimic facial behavior in face-to-face communication. Presumably, this allowed the participants greater control over their expression.

There's little doubt that emoticons have improved the communication abilities of texters, emailers, and chatters worldwide, but have they done so to the detriment of our actual ability to write? I'll let you mull this over.

In the meantime, I'm going to go (>'_')>#.

(That means have a waffle.)

June 2012 Archives

Science Behind Five Weird Gardening Tips

Chateau_de_Bouges_Flower_Garden_1.jpgPhoto by SiefkinDR via Wikimedia Commons

As we turn the corner into summer, I see more and more people outside in their gardens. Nurseries are swarming with gardeners looking to brighten their beds with annuals. The more ambitious souls are toiling in their vegetable patches.

I, for one, struggle to keep an indoor cactus alive, so I am hesitant to grow anything requiring more complex maintenance. But I still like learning about how others conjure their botanical masterpieces. And who knows-- maybe a little science is just what I need to go outside and get my hands dirty.

1) Don't touch

Some plants, like gardenias, are very sensitive to touch. A slight poke or even splashed water can bruise the petals of this wimpy plant. But research has shown that gardenias might not the only plants that are touchy.

A team of ecologists who were collecting measurements became concerned when half of the plants they were studying started to die. After some thought, they realized that by touching the plants to collect their data they could be causing the problem themselves.

Intrigued, the researchers designed a new experiment where they systematically stroked different varieties of weeds in order to simulate the handling of plants during data collection. For one variety, the stroked plants seemed to be more susceptible to insect attacks compared to the control plants. With another variety, however, the handled plants were more resistant to bugs than the control. Therefore it's possible that poking and prodding plants cause them to release chemicals that either attract or repel pests.

2) Try some blood

It's probably not a good idea to sprinkle your garden with human blood, but animal blood is OK. In fact, it is encouraged. You can even buy animal blood in a powder form called bloodmeal. It seems the makers of this appetizing product simply collect blood from slaughterhouses, remove the impurities, dry it using a spraying technique, and package it up.

Some gardeners use bloodmeal to keep the pests away. Believe it or not, the stuff doesn't smell very good, so the deer and rabbits will leave your plants alone.

Blood also has a lot of protein in it, making it a good fertilizer. Soil bacteria break down the protein into ammonia, which plants absorb through their roots to use as a source of nitrogen.

3) Use your resources

Another body fluid can also be used as fertilizer. Yep, peeing on your garden can actually be beneficial. This time, the nitrogen is provided in the form of urea, which soil bacteria also convert to ammonia so it can be taken up by plants.

One study found that treating tomato plants with a mixture containing human urine quadrupled the plants' fruit production. The unique fertilizer even made the tomatoes taste different from tomatoes grown with traditional fertilizer, but apparently the tasters didn't prefer either variety over the other.

4) Freshen cut flowers with pennies

People have tried using a lot of substances to keep cut flowers looking happy--aspirin, vodka, and bleach to name a few. These three work by killing bacteria or fungus that may invade the newly-severed stems.

Another suggestion is to put a penny in the vase. I was skeptical of this idea until I learned that copper also works as bactericide and fungicide. In fact, copper is one of the oldest fungicides in the book, and it is still used today (often by organic farmers).

Copper targets essential enzymes the fungus needs. In fact, copper disrupts not just one enzyme but many, making it a multi-site fungicide. This property distinguishes it from a lot of modern synthetic fungicides, which only act on one specific enzyme. What's more, copper's multi-site abilities make it a lot more difficult for a fungus to become resistant to it.    

5) Prune wisely

To me, chrysanthemums are fascinating because different varieties can produce very different flowers. Some mums are a brushy mess of small florets; others consist of a large, solitary flower. This variety in flower size and number is due in part to how the mums are pruned as they grow.

In order to make a bushy, many-flowered plant, you pinch off the mums' top buds so that the side branches get a chance to grow their own flowers. To get a large, single flower you prune or, as it's called in this case, "disbud" the side branches so that the mum's efforts are all concentrated toward one flower. 

But how does a plant know how to respond to pruning? Research shows that the main (usually top) bud of the plant normally releases plant hormones to inhibit growth at the side buds. The top bud's strategy is to squelch any competition for the plant's resources. But when the top bud is chopped off, the side buds are free to grow.

June 2012 Archives

'Mousetronauts' Help Prepare Humans to Go to Mars

It was one minute before midnight on August 28th, 2009 when Space Shuttle Discovery blasted off from Cape Canaveral, riding a wave of fire into the moonlit sky. The mission -- STS-128 -- was yet another glorious trek for mankind into outer space, and an even more intrepid endeavor for mousekind. Six bold mice -- mousetronauts if you will -- flew into space that day inside the Mice Drawer System (MDS), a mechanized enclosure designed to house mice with minimal maintenance from the astronauts on board the International Space Station. Think of it as a tiny hotel. Together, the MDS and the mice were integral parts of an experiment designed to study the effects of microgravity on mammals.

MDS4.jpgNASA astronaut Nicole Stott shows off the MDS. (NASA image)

During the experiment, two of the rodent inhabitants died for health-related reasons and another passed away due to a malfunction with the MDS. But the three other mice survived 91 days on board the International Space Station, a record for non-human mammals.

Nineteen separate investigations from scientists representing six different countries were conducted in conjunction with the MDS experiment, and their results are just starting to be published for all to see.

On May 29th, the open access journal PLoS ONE launched the Mice Drawer System Experiment Collection, which will bring together many of the articles drawn from the pioneering project. Already, four papers have been published from the MDS experiment, with results that will undoubtedly benefit humans as we strive to adapt to longer duration spaceflights.

One recently published study looked at alterations in hormone levels tied to space-induced changes on the thyroid and testis. Another examined spaceflight-induced changes in cell membrane composition and antioxidant defenses and how they relate to preventing a condition called "space anemia." The study also laid the groundwork for future research on how to reduce oxidative stress and space anemia, possibly through dietary supplementation.

floating mouse.jpgA mousetronaut floats around in its MDS compartment. (Photo from PLoS One)

Perhaps the most important MDS study published to date looked at transgenic mice modified to produce extra pleiotrophin (PTN) - a protein involved in bone development. The study found that mice producing extra PTN were partially protected from serious losses in bone density. This result grants some insight on how bone loss can be mitigated for astronauts spending long bouts in space. Commonly, they can experience as much as a 20 to 30 per cent reduction in bone density on an extended mission due to the effects of living in a microgravity environment.

More of the MDS studies are slated to be published soon. We can look forward to seeing research into microgravity's effects on brain tissue, the heart muscle, the immune system, as well as circadian rhythms and metabolic systems.

One of the ultimate hopes is that the unprecedented amount of data created from the MDS experiment will eventually lead to methods to minimize the detrimental effects of microgravity on the human body, thus opening the door for long distance spaceflight to Mars and beyond.


Citation: The Mice Drawer System Experiment and the Space Endurance Record-Breaking Mice (2012) PLoS Collections: http://www.ploscollections.org/Mice_Drawer_System