By Eliza Strickland
What can you learn from getting your genome sequenced? If you’re a relatively healthy person like me, the answer is, not much… at least not yet.
I embarked on a mission to get myself sequenced for my recent article “The Gene Machine and Me.” The article focused on the sequencing technology that will soon enable a full scan of a human genome for $1000, and to make the story come alive, I decided to go through the process myself. I got my DNA run through the hottest new sequencing machine, the Ion Proton, and had it analyzed by some of the top experts on genome sequencing, a team at Houston’s Baylor College of Medicine.
The Baylor team has been intimately involved in many of the most important advances of genome sequencing over the last decade. And their accomplishments reveal both the astoundingly rapid progress of the technology, and how far we have yet to go. Here’s a synopsis: the story of five genomes.
By Carrie Arnold
Those with a sensitive sniffer are treated to the pleasure of subtle differences between an ’84 Bordeaux and an ’87 Cabernet, or the ability to tell whether the diner down the street is having a special on onion rings or fries. Even the non-foodies among us can tell whether a carton of milk has expired with a single sniff. But new research hints that the function of taste and smell receptors go far beyond our gourmand aspirations. Scientists have found that the proteins we use to detect certain tastes and scents are actually an important part of our immune system.
Of all the classes of taste (sweet, sour, salty, bitter and umami), humans are the best at detecting bitter, and for good reason. Many of the toxins found in food are bitter, and being able to sense these in minute qualities was a great evolutionary boon to staying alive and healthy. Not surprisingly, bitter taste receptors are found in large quantities on the tongue. But a 2009 study in Science also found these receptors deep in the lungs. Otorhinolaryngologist and sinus surgeon Noam Cohen at the University of Pennsylvania went spelunking through the nose—his area of expertise—to see whether it might contain the same receptors, and found that it did.
By Pete Etchells
I was a gamer kid. Heck, I still am a gamer kid. And like any form of media, old or new, video games have had their fair share of negative airtime. Much like how comic books were vilified in the 1950s for corroding young and impressionable minds (although the research behind those claims is now in dispute), video games are similarly being scrutinized for their effects on development and behavior.
But a relatively new branch of science is focusing on the therapeutic aspects of video games. This new generation of researchers who have grown up with video games are starting to use their unique mix of skills to look into the possibility of improving people’s lives through gaming. And there’s three promising areas where games appear to have a unique leg up on traditional therapies.
Scott Firestone works as a researcher in evidence-based surgery, and recently started blogging about public health and environmental issues at His Science Is Too Tight, where this post originally appeared. You can find him on Twitter at @scottfirestone.
Kevin Drum from Mother Jones has a fascinating new article detailing the hypothesis that exposure to lead, particularly tetraethyl lead (TEL), explains the rise and fall of violent crime rates from the 1960s through the 1990s—at which point the compound was phased out of gasoline worldwide. It’s a good bit of public health journalism compared to much of what you see, but I’d like to provide a little bit of epidemiology background to the article. There’s so many studies listed that it’s a really good intro to the types of study designs you’ll see in public health. It also illustrates the concept of confirmation bias, and why regulatory agencies seem to drag their feet even in the face of such compelling stories as this one.
Drum correctly notes that the correlation is insufficient to draw any conclusions regarding causality. The research (pdf) published by economist Rick Nevin was simply looking at associations, and saw that the curves were heavily correlated, as you can quite clearly see. When you look at data involving large populations, such as violent crime rates, and compare with an indirect measure of exposure to some environmental risk factor such as levels of TEL in gasoline during that same time, the best you can say is that your alternative hypothesis of there being an association (null hypothesis always being no association) deserves more investigation. This type of design is called a cross-sectional study, and it’s been documented that values for a population do not always match those of individuals when looking at cross-sectional data.
Keith Kloor is a freelance journalist whose stories have appeared in a range of publications, from Science to Smithsonian. Since 2004, he’s been an adjunct professor of journalism at New York University. You can find him on Twitter @KeithKloor.
Last month, a group of Massachusetts residents filed an official complaint claiming that the wind turbine in their town is making them sick. According to the article in the Patriot Ledger, the residents “said they’ve lost sleep and suffered headaches, dizziness and nausea as a result of the turbine’s noise and shadow flicker [flashing caused by shadows from moving turbine blades].” A few weeks later, a story from Wisconsin highlighted similar complaints of health problems associated with wind turbines there.
Anecdotal claims like these are on the rise and not just in the United States. A recent story in the UK’s Daily Mail catalogs a litany of health ailments supposedly caused by wind turbines—everything from memory loss and dizziness to tinnitus and depression.
I expect so. For one thing, the alleged health problem has been adopted by demagogues and parroted on popular climate-skeptic websites. But the bigger problem is that “wind turbine syndrome” is what is known as a “communicated” disease, says Simon Chapman, a professor of public health at the University of Sydney. The disease, which has reached epidemic proportions in Australia, “spreads via the nocebo effect by being talked about, and is thereby a strong candidate for being defined as a psychogenic condition,” Chapman wrote several months ago in The Conversation.
What Chapman is describing is a phenomenon akin to mass hysteria—an outbreak of apparent health problems that has a psychological rather than physical basis. Such episodes have occurred throughout human history; earlier this year, a cluster of teenagers at an upstate New York high school were suddenly afflicted with Tourette syndrome-like symptoms. The mystery outbreak was attributed by some speculation to environmental contaminants.
But a doctor treating many of the students instead diagnosed them with a psychological condition called “conversion disorder,” as described by psychologist Vaughan Bell on The Crux:
A new toxicology study states that rats eating genetically modified food and the weedkiller Roundup develop huge tumors and die. But many scientists beg to differ, and a close look at the study shows why.
Genetically modified organisms (GMOs) have always been a controversial topic. On the one hand are the many benefits: the higher crop yields from pesticide- and insect-resistant crops, and the nutritional modifications that can make such a difference in malnourished populations. On the other side is the question that concerns many people: We are modifying the genes of our food, and what does that mean for our health? These are important question, but the new study claiming to answer them misses the mark. It has many horrifying pictures of rats with tumors, but without knowledge about the control rats, what do those tumors mean? Possibly, nothing at all.
The recent study, from the Journal of Food and Chemical Toxicology has fueled the worst fears of the GMO debate. The study, by Italian and French groups, evaluated groups of rats fed different concentrations of maize (corn) tolerant to Roundup or Roundup alone, over a two year period, the longest type of toxicology study. (For an example of one performed in the U.S., see here.) The group looked at the mortality rates in the aging rats, as well as the causes of death, and took multiple samples to assess kidney, liver, and hormonal function.
The presented results look like a toxicologist’s nightmare. The authors reported high rates of tumor development in the rats fed Roundup and the Roundup-tolerant maize. There are figures of rats with visible tumors, and graphs showing death rates that appear to begin early in the rats’ lifespan. The media of course picked up on it, and one site in particular has spawned some reports that sound like mass hysteria. It was the first study showing that genetically modified foods could produce tumors at all, let alone the incredibly drastic ones shown in the paper.
Neuroskeptic is a neuroscientist who takes a skeptical look at his own field and beyond at the Neuroskeptic blog.
Life is dominated by the Earth’s cycles. Day and night, spring and autumn, change the environment in so many ways that almost all organisms regulate their activity to keep up with time and the seasons. Animals sleep, and many hibernate, moult, and breed only at certain times of the year. Plants time the growth of seeds, leaves, fruit and shoots to make the most of the weather.
But what about humans? We sleep, and women menstruate, but do other biological cycles affect our behavior? The Internet has offered researchers a unique resource for answering this question.
For example, according to research published recently in the Archives of Sexual Behavior from American researchers Patrick and Charlotte Markey, Americans are most likely to search for sex online during the early summer and the winter.
The authors looked at the Google Trends for a selection of naughty words and phrases, and this revealed a pretty marked 6 month cycle for searches originating from the USA, with two yearly peaks in the search volumes. The words were related to three categories: pornography, sex services (e.g. massage parlors), and dating websites.
Google Trends searches for pornography-related words over time
This image shows the graph for pornography searches—the grey line—with an idealized six-month cycle also shown for comparison, the black line. The data show a strong twice-yearly peak. The picture was similar for two other categories of sexual words: prostitution and dating websites.
Jesse Bering, PhD, is regular contributor to Scientific American, Slate, and other publications. He is the author of the recently released book, Why Is the Penis Shaped Like That? And Other Reflections on Being Human and The Belief Instinct, which the American Library Association named one of the “25 Best Books of 2011.” You can find him here.
For the past seven years, I’ve been in an “interpenile relationship”—I, the lesser of the two you might say, am circumcised; my partner is not. This contrast between our members is not exactly at the top of our list of concerns. But it is nonetheless interesting how my prepuce came to disappear into a medical waste bin in a bustling New Jersey hospital on some springtime day in 1975, whereas his, by contrast, has remained a fellow traveler all the long way from that tiny Mexican village where he slipped from his young mother’s womb on a chilly December morning in 1981. That womb, incidentally, belonged to a Roman Catholic. The one that I bathed in, the place in which I had my “bones and sinews knitted together,” in the words of Job, was the property of a Jew. So despite neither of us being particularly patriotic nor, certainly, religious today, the organs dangling so differently between us are nevertheless the very incarnations of our parents’ vast cultural differences.
Whatever the reasons that previous generations may have had for choosing to remove their infant sons’ foreskins, they were almost always unconvincing. All else being equal—and let me reiterate that caveat because it’s likely to go unnoticed, with some readers eagerly pointing out to me those rare cases of congenital defects in which circumcision can legitimately improve the quality of life for some males, which is of course true—all else being equal, any dubious benefits derived from religious, social, hygienic, or aesthetic reasons are clearly outweighed by the costs of male circumcision. Because of some rabbi in Hackensack shaking his head over my intact genitalia, my parents went unblinkingly along with the amputation of a fully operational, perfectly healthy, and probably adaptive body part, all to sacrifice an ounce of their son’s tender flesh to a god that he would never believe in anyway.
Today, however, all is no longer equal, and the balance between the relative risks and benefits of male circumcision has clearly shifted in the other direction. That is, it has according to the American Academy of Pediatrics, which just earlier this week put out its revised position statement on infant male circumcision. Here’s the money quote:
Systematic evaluation of English-language peer-reviewed literature from 1995 through 2010 indicates that preventive health benefits of elective circumcision of male newborns outweigh the risks of the procedure. Benefits include significant reductions in the risk of urinary tract infection in the first year of life and, subsequently, in the risk of heterosexual acquisition of HIV and the transmission of other sexually transmitted infections.
Many of our parents, it seems, may have actually made the right decision for the wrong reasons. Although the task force behind the Academy’s reassessment stopped short of advising “routine” and “universal” removal of the foreskin for all newborn males, and stressed that it remains a personal decision to be made by informed parents, its language represents an increasingly unambiguous endorsement of male circumcision among the world’s leading health organizations (including the World Health Organization and UNAIDS) . By contrast, many of the world’s leading parents remain skeptical of the findings reviewed by the Academy, questioning both the methodologies and the generalizability of studies conducted overwhelmingly with African populations, in which rates of infection are dramatically higher than those in the US. (For more information on this research, as well as a description of the physical factors responsible for the reduction of HIV acquisition in circumcised males, see my earlier discussion at Scientific American.) The more vocal “intactivists,” who’ve long been protesting what they regard as an antiquated, cruel and unnecessary ritual act against little boys that is just as abhorrent as female clitoridectomy, have also responded bitterly to this newest AAP development, seeing fresh strands in an ongoing web of conspiracy between the major health organizations, third-party insurance companies implementing the policy views of these organizations, and greedy practitioners who mislead parents about the benefits of circumcision only to reap insurance payouts for “mutilating” children’s genitals.
Derek Lowe is a medicinal chemist who has worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer’s, diabetes, osteoporosis, and other diseases. He has been writing about drug discovery at In the Pipeline, where this post originally appeared, for more than ten years.
The British Medical Journal says that the “widely touted innovation crisis in pharmaceuticals is a myth.” The British Medical Journal is wrong.
There, that’s about as direct as I can make it. But allow me to go into more detail, because that’s not the the only thing they’re wrong about. This is a new article entitled “Pharmaceutical research and development: what do we get for all that money?”, and it’s by Joel Lexchin (York University) and Donald Light of UMDNJ. And that last name should be enough to tell you where this is all coming from, because Prof. Light is the man who’s publicly attached his name to an estimate that developing a new drug costs about $43 million dollars.
I’m generally careful, when I bring up that figure around people who actually develop drugs, not to do so when they’re in the middle of drinking coffee or working with anything fragile, because it always provokes startled expressions and sudden laughter. These posts go into some detail about how ludicrous that number is, but for now, I’ll just note that it’s hard to see how anyone who seriously advances that estimate can be taken seriously. But here we are again.
Andres Barkil-Oteo is an assistant professor of psychiatry at Yale University School of Medicine, with research interests in systems thinking, global mental health, and experiential learning in medical education. Find him on Google+ here.
Last spring, the American Psychiatric Association (APA) sent out a press release [pdf] noting that the number of U.S. medical students choosing to go into psychiatry has been declining for the past six years, even as the nation faces a notable dearth of psychiatrists. The Lancet, a leading medical journal, wrote that the field had an “identity crisis” related to the fact that it doesn’t seem “scientific enough” to physicians who deal with more tangible problems that afflict the rest of the body. Psychiatry has recently attempted to cope with its identity problem mainly by assuming an evidence-based approach favored throughout medicine. Evidence-based, however, became largely synonymous with medication, with relative disregard for other evidence-based treatments, like some forms of psychotherapy. In the push to become more medically respected, psychiatrists may be forsaking some of the important parts of their unique role in maintaining people’s health.
Over the last 15 years, use of psychotropic medication has increased in all kinds of ways, including off-label use and prescription of multiple drugs in combination. While overall rates of psychotherapy use remained constant during the 1990s, the proportion of the U.S. population using a psychotropic drug increased from 3.4 percent in 1987 to 8.1 percent by 2001. Antidepressants are now the second-most prescribed class of medication in the U.S., preceded only by lipid regulators, a class of heart drugs that includes statins like Lipitor. Several factors have contributed to this increase: direct-to-consumer advertising; development of effective drugs with fewer side effects (e.g., SSRIs); expansion in health coverage for mental illness made possible through the Mental Health Parity Act; and an increase in prescriptions from non-psychiatric physicians.
Unfortunately, not all of these psychiatric drugs are going to good use. Antidepressive drugs are widely used to treat people with mild or even sub-clinical depression, even though drugs tend to be less cost-effective for those people. It may sound paradoxical, but to get more benefit of antidepressants, we need to use them less, and only when needed, for moderate to severe clinically depressed patients. Patients with milder forms should be encouraged to try time-limited, evidence-based psychotherapies; several APA-endorsed clinical guidelines center on psychotherapies (e.g., cognitive behavioral therapy or behavior activation) as a first-line treatment for moderate depression, anxiety, and eating disorders, and as a secondary treatment to go with medication for schizophrenia and bipolar disorder.