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Gut Bacteria, Obesity

In 1977, National Lampoon parodied Scientific American as “Scienterrific American.” I think they were on to something. I’ve written a few posts about whether we should trust scientists, whether scientists can trust each other, etc. Sadly, some scientists will publish what they are paid to publish, and some will publish whatever makes headlines, so they can continue to work. Some of their results are not reproducible, which means they aren’t really doing science. The charitable view is that eventually the scientific method will sort out the scientific from the scienterrific, but a lot of us were ingesting PFOA from Teflon long before we were told that it was a carcinogen.

Recent headlines advised that the FDA had banned sales of many antibacterial soaps, containing any of over a dozen chemicals, because “the risks outweigh the benefits.”

Studies in animals have shown that triclosan and triclocarban can disrupt the normal development of the reproductive system and metabolism, and health experts warn that their effects could be the same in humans. The chemicals were originally used by surgeons to wash their hands before operations, and their use exploded in recent years as manufacturers added them to a variety of products, including mouthwash, laundry detergent, fabrics and baby pacifiers. The Centers for Disease Control and Prevention found the chemicals in the urine of three-quarters of Americans.

That New York Times article notes that a trade group, The American Cleaning Institute, opposes the FDA ruling, and claims to have studies that support their opposition. I’m sure they do.

Scientific American (the real one) has posted an excerpt of a book, Let Them Eat Dirt: Saving Your Child from an Oversanitized World, written by two microbiologists: B. Brett Finlay, Ph.D., and Marie-Claire Arrieta, Ph.D.

Finlay and Arrieta point out that while antibiotics have certainly saved many, many of us from dying young from an infectious disease, they have also changed our environment in more subtle ways. Besides the fear about developing unstoppable superbugs, we may be making ourselves susceptible to a raft of non-infectious diseases. One concern is the use of antibiotics in meat, another is the use of antibiotics in early childhood:

While these studies didn’t prove that antibiotics directly cause obesity, the consistency in these correlations, as well as those observed in livestock, prompted scientists to have a closer look. What they found was astonishing. A simple transfer of intestinal bacteria from obese mice into sterile (“germ-free”) mice made these mice obese, too! We’ve heard before that many factors lead to obesity: genetics, high-fat diets, high-carb diets, lack of exercise, etc. But bacteria—really? This raised skepticism among even the biggest fanatics in microbiology, those of us who tend to think that bacteria are the center of our world. However, these types of experiments have been repeated in several different ways and the evidence is very convincing: the presence and absence of certain bacteria early in life helps determine your weight later in life. Even more troubling is the additional research that shows that altering the bacterial communities that inhabit our bodies affects not just weight gain and obesity, but many other chronic diseases in which we previously had no clue that microbes might play a role.


About a month ago, I read Middlesex, the Pulitzer prize-winning novel by Jeffrey Eugenides, whose first novel was The Virgin Suicides. I had seen the film version of Suicides, directed by Sofia Coppola, but that isn’t why I bought Middlesex.

The voice of Middlesex is a person whose anatomy is not easily identified as male or female, what has come to be termed intersex. I have a child who, though not physiologically intersex, has been influenced by Simon Baron-Cohen’s Empathizing-Systemizing theory which holds that autism spectrum disorder, or Asperger’s syndrome, leads to an extreme male brain (EMB). As described in a 2011 post on Woman with Asperger’s, some female Aspies do feel in between:

While I am biologically female, I have never felt at home in the world of women. I have trouble understanding and socializing with most neurotypical women, and I am not interested in the same things that they are: I’d rather talk about the Enneagram or philosophy than about the latest gossip in the mill. My sense of fashion and style has come from years of observation, developing my own color palettes (I find that black, purple, blue, red, gold, and silver are each to match with each other), finding comfortable fabrics and shoes, and making a lot of mistakes, and it did not come natural to me; you are looking at the girl who was more interested in Greek mythology and African-American poetry than fixing her hair, which used to drive the aunt who raised me to distraction. And as I have mentioned before, I have empathy but lack the ability sometimes to decode the signals of what people are feeling and what they might need. Truthfully, I do almost feel half-female, half-male as Simone described above – for example, I have a primary male alter-ego who finds himself as the speaker in about a good third of my poems.

But EMB is a controversial theory, as described in a 2013 post on Musings of an Aspie:

There are a lot of holes in the EMB theory. It bases maleness and femaleness on a single pair of traits, which aren’t even mutually exclusive. It subscribes to outdated gender stereotypes of men as less nurturing and women as less logical/intellectual. It uses questionnaires designed by the researcher to prove the researcher’s point. It fails to even acknowledge the existence of nonbinary gender identity (which is especially significant in autistic populations, as mentioned later in this post). It completely ignores the possibility that females are simply underdiagnosed, which undermines the protective effect line of thinking. It uses characteristics of autism as a proxy for gender traits, thereby “proving” a link between gender and autism.

I have read my child’s prolific fan-fiction writings, and they strike me as coming from a female perspective, but it isn’t my journey. So I’m trying to read up on intersex and transgender issues.

Intersexuality is a very uncomfortable topic, as evidenced by all the people arguing over who uses which bathroom. I guess some people simply don’t know the difference between transvestites, who simply wear clothing of the opposite sex, and transgender people, who have changed their bodies to become the opposite sex. Others do know the difference, but enjoy being mean.

3 Quarks Daily featured an article in Nature, The spectrum of sex development: Eric Vilain and the intersex controversy. DSD is short for Disorders of Sex Development. It’s a good article:

Vilain has spent the better part of his career studying the ambiguities of sex. Now a paediatrician and geneticist at the University of California, Los Angeles (UCLA), he is one of the world’s foremost experts on the genetic determinants of DSDs. He has worked closely with intersex advocacy groups that campaign for recognition and better medical treatment — a movement that has recently gained momentum. And in 2011, he established a major longitudinal study to track the psychological and medical well-being of hundreds of children with DSDs.

Vilain says that he doesn’t seek out controversy, but his research seems to attract it. His studies on the genetics of sexual orientation — an area that few others will touch — have attracted criticism from scientists, gay-rights activists and conservative groups alike. He is also a medical adviser for the International Olympic Committee, which about five years ago set controversial rules by which intersex individuals are allowed to compete in women’s categories.

But what has brought Vilain the most grief of late has been his stance on sex-assignment surgery for infants with DSDs. Although he generally opposes it, he won’t categorically condemn it or the doctors who perform it. As a result, many intersex advocates who object to the practice now see him as a hindrance to their cause.

Some deaf people have embraced their lack of hearing as normal for them, and assert that cochlear implant surgery separates deaf children from the mainstream of deaf culture. Similarly, some intersex people oppose any sort of corrective surgery on infants or children as not normal for them, and as rife with disastrous realizations later in life. In some ways, Middlesex is a very long explanation of that point-of-view.

Chernobyl after thirty years

Thirty years ago, the staff running a test on reactor #4 at the Lenin Nuclear Power Plant near Pripyat, Ukraine, USSR were reading unexpectedly high radiation levels. They debated stopping the test, but decided to keep going to find the limits. When the temperature readings climbed too high as well, they tried to shut the reactor down by inserting carbon rods.

There was, however, a design flaw, known by upper levels in the government, but not by the staff doing the testing. Inserting those rods somehow increased the reaction, increasing the heat. Containment water became steam, the roof of the reactor blew off and some ten tons of radioactive uranium became airborne, and was carried southeast, contaminating a large swath of Europe.

McClatchy has a very good article, Ruined Chernobyl nuclear plant will remain a threat for 3,000 years, in which they actually mention other nuclear accidents:

What they figured out was the worst nuclear-energy disaster in human history, far worse than the explosion at Kyshtym nuclear complex in 1957 in what was then the Soviet Union, which released 70 tons of radioactive material into the air, or the 1957 fire at the Windscale Nuclear Reactor in northwestern England, which forced a ban on milk sales for a month, or the Three Mile Island disaster in Pennsylvania on March 29, 1979, where a cooling malfunction led to a partial meltdown.

There are also persistent leaks threatening groundwater at Hanford in the US, and the ongoing Fukushima disaster in Japan.

CNN tries to consign the radiation problems to history, offering more upbeat articles about Chernobyl. In Meet the New Face of Chernobyl they focus on fetching young Yulia, who lives in a nearby community, Slavutych, and was chronicled over three years by Swiss photographer Neils Ackermann:

Ackermann isn’t interested in making you sit through another telling of that tragic tale about the firefighters who couldn’t put out the flames in 1986, or the technicians who failed to stop the poisonous radioactive particles from escaping the facility and raining down on nearby residents.

Instead, he wants to introduce you to Yulia.

“She’s intense, like an energy bomb,” Ackermann said, describing the 23-year-old woman he met in 2012. At the time, Yulia was kissing a man in a park in the center of Slavutych, a town near Chernobyl built for disaster evacuees.

Yulia was born three years after the disaster. Ackermann once asked her what she thought about its consequences. “She was looking at me like it was a really stupid question,” he recalled. “Because now, the scale of health consequences resulting from radioactivity in Slavutych are much more limited than what we may think about in the West.” Slavutych residents who work in Chernobyl are protected by strict control systems. The town’s attitude about radioactivity is much more realistic and pragmatic than it would be elsewhere. One young man showed Ackermann the tomb of his best friend in a cemetery and said more people in town die because of drugs and alcohol than radioactivity.

In another article, CNN emphasizes the precautions taken as Ukraine builds a new arched structure over the decrepit sarcophagus that was built quickly after the explosion. This New Safe Confinement structure is supposed to last at least one hundred years, but the buried mass will be a threat for at least three thousand years, so I wonder who will build the next thirty structures?

Zika Doubts

Actor and prolific social media maven George Takei took some heat last week for promoting a post that claimed that the numerous cases of microcephaly seen in Brazil may have been caused by an insect growth inhibitor called Pyriproxyfen, rather than by the Zika virus. Scientists swear that that particular chemical is not dangerous to humans. Given the lack of oversight of the chemical industry, there is very little trust in such pronouncements, but there is no clear evidence linking Pyriproxyfen to microcephaly.

The evidence in favor of a connection between Zika and microcephaly is stronger, but not yet proven: Some dead microcephalic babies have been found with the virus in their brains, or in their amniotic fluid. Some mothers of microcephalic babies have been infected with Zika. But there are also sound reasons to doubt whether Zika is related to the microcephaly in Northeast Brazil.

First of all, despite heart-rending pictures of babies with almost no foreheads, it isn’t that clear that there has actually been an increase in microcephaly. Definitions of microcephaly vary between doctors. Medical statistics kept in that area are not that thorough or reliable. Also, some attribute the epidemic to the awareness effect, and suspect that microcephaly hasn’t attracted much attention before.

Second, one bit of research may indicate that an increase in microcephaly began in 2012, two years before the recognition of the increase in Zika virus. It may be that Zika began to increase earlier than noticed, or it may be that the two are unrelated.

Third, Zika outbreaks in other regions have not been shown to correspond to more cases of microcephaly. Again, there may be bad reporting and varying definitions of microcephaly in those regions, or there may be no connection.

And fourth, as noted in FiveThirtyEight’s, Why It’s So Hard To Prove Zika Is Causing Birth Defects:

Zika would not be the first virus to lead to microcephaly — rubella can also cause the condition — but it would be the first virus of its kind known to trigger it. Other flaviviruses, such as dengue and West Nile, are not known to cause microcephaly, and that’s perplexing, said Moore, the RAND pediatrician. “There are plenty of other viruses in this family, and none of them cause this.”


Blood Clots in Fit Legs

In 2011, Serena Williams, one of the greatest athletes in history, suffered a pulmonary embolism, was treated for that, then suffered a hematoma. Soon after winning Wimbledon for the fourth time, Serena cut her foot on a shard of glass, needing eighteen stitches to close the wound. Some combination of her injury and/or her resulting inactivity and/or a long flight from New York to Los Angeles led to a deep venous thrombosis (DVT), and some of the clotting material travelled through her bloodstream to a pulmonary artery, causing an embolism of her lung.

About a year ago, on a very cold morning, I biked down the hill, then tore a big muscle in my left thigh when I stepped up with my bike onto the light rail. My leg healed over the spring, and I commuted by bike almost every day all summer and fall and into the mild winter. It got cold a few weeks before the record setting snow fall, and I decided to begin walking down the hill to the station, walking back up in the evenings. I walk a lot, so I didn’t have any problems at first.

For a few days after the snowfall, I had to walk a lot further because light rail and buses stopped three miles from my office. Descending and climbing the hill was a chore because there was hardly any shoulder left for walking. Over Superbowl weekend, my old thigh injury began to ache. In a few days, my left calf began to feel tight. I assumed I was favoring the upper leg and had overused the calf, so I began taking the bus up and down the hill.

But after a week of limping between bus and light rail, I saw that my left calf was swollen. My right calf is 18 inches around, but the left one had increased to just over 20 inches. My wife reported my symptoms to my local physician, who urged me to get to the emergency room. The PA in the ER didn’t think I fit the profile of DVT, and neither did I, but an ultrasound exam found a clot just below and behind my left knee.

They prescribed the very expensive Xarelto, which wasn’t covered by my insurance plan, and I rested the leg at home for four days. For the last three days I have been driving a rental car to rest the leg as much as possible while still working to afford the bills that will soon be arriving for the ER visit. Next week I am to visit a vascular surgeon who will advise me on whether the clot should be removed surgically.

[Update 20160225: The vascular surgeon recommended that I continue on blood thinner for several months, wear a knee high compression sock during the day, and resume exercising. That’s good news.]

I have found several articles about endurance athletes getting DVT. It isn’t common, but it isn’t as uncommon as one might think, either. In, Hidden danger: DVT in endurance athletes, advises:

Some people are familiar with the potential for DVT to occur during or after a long airplane flight. This has been referred to “Economy Class Syndrome.”

Did you know that 85% of air travel thrombosis victims are athletic, usually endurance athletes?

Being a cyclist is no guarantee against clotting:

So what does this have to do with riding a bicycle? Bicycle riders typically are in good shape, watch what they eat, and take care of themselves. They are not generally overweight. If they have been riding for some time and cover 300 miles or more a month at a good pace, their resting heart rate is generally lower than the norm for their age.

Lower resting heart rate means slower blood flow throughout the body. This is especially true for those riders who participate in endurance events such as century rides, time trials, and other competitive events.

Slower blood flow — sound familiar?

Unfortunately, that slower blood flow that is great for your heart can work against you if you have mostly sedentary work, as I do. Most days I sit at the computer only getting up to go to the rest room or print room, or chat with a coworker. A little riding in the morning and an hour in the evening is better than nothing, but my life is still fairly sedentary.

Teflon, Diesels, Toxins, Cancer

I’m probably not the only one wondering whether some of these celebrities recently died in their late sixties because of smoking, using drugs, or just from being immersed in a sea of carcinogens like the rest of us. You might think the EPA protects us by labeling carcinogens, but they only test a small percentage of chemicals in use. For example, perfluorooctanoic acid, or PFOA, or C8, a key substance in Teflon, was not tested until one law firm brought a lawsuit on behalf of some farmers downstream of a dump site.

The Lawyer Who Became DuPont’s Worst Nightmare

‘‘Rob’s letter lifted the curtain on a whole new theater,’’ says Harry Deitzler, a plaintiff’s lawyer in West Virginia who works with Bilott. ‘‘Before that letter, corporations could rely upon the public misperception that if a chemical was dangerous, it was regulated.’’ Under the 1976 Toxic Substances Control Act, the E.P.A. can test chemicals only when it has been provided evidence of harm. This arrangement, which largely allows chemical companies to regulate themselves, is the reason that the E.P.A. has restricted only five chemicals, out of tens of thousands on the market, in the last 40 years.

… if you are a sentient being reading this article in 2016, you already have PFOA in your blood. It is in your parents’ blood, your children’s blood, your lover’s blood. How did it get there? Through the air, through your diet, through your use of nonstick cookware, through your umbilical cord. Or you might have drunk tainted water. …

Bertel Schmitt used to blog at The Truth About Cars (as did I), now blogs at the Daily Kanban, and in Forbes Magazine, writes: Dieselgate Now Officially An Industry-Wide Problem As Cancer Worries Mount

Nitric oxide NO, nitrogen dioxide NO2, and nitrous oxide N2O (as a group called NOx) are released by many forms of combustion. Over half of NOx is released by internal combustion engines, particularly diesels. Volkswagen’s falsifying of their emissions tests has brought renewed attention to NOx, a carcinogen that I breathe every time I bike behind a bus.

The driving force behind it is German lobby group Deutsche Umwelthilfe, which through its member Axel Friedrich, a former official of Germany’s EPA-equivalent Umweltbundesamt, is connected with the International Council on Clean Transportation (ICCT), the NGO that helped unravel Volkswagen’s dieselgate in America. For years, the group has tried to draw attention to the fact that NOx causes cancer, and that it is, according to the WHO, as dangerous as asbestos. Now, as Reuters writes, “the diesel scandal has heightened awareness of real-world NOx emissions by the broader auto industry,” and the message of the campaigners is beginning to resonate.

Older Bike, Younger Knees

In April I wrote about experiencing more and more knee pain after several years of riding my 2004 Xootr Swift increasingly longer distances, and more frequently, to work. One of the problems was that the clamps holding the saddle weren’t tight enough. Even if I got the saddle at the right height after unfolding, it could slowly slide down while I was riding. Fixing the saddle at the proper height with a clamp, was an improvement – but not enough.

In August, I heard/felt a noise from the rear wheel. I saw that a three inch segment of the Swift’s rear rim was pushing out and grabbing the pad during every rotation. While Light St Cycles was working on that in Baltimore, I had my 1988 Trek 1100, a full size road bike, refurbished at Pedal Power in Altoona. I brought the Trek to Baltimore and started riding it to and from work. The dimensions of the Trek are almost identical to those of my custom-fit Serotta, and I soon noticed that my knees weren’t hurting after commuting on the Trek every day.

A cycling buddy at work advised me that saddle height was important, but so were ‘stack’ and ‘reach’ – which define the distance from the pedal hub to the handlebars. I measured, and the Swift’s reach is much shorter than my other bikes. I could have tried a much longer handlebar stem, but instead I have just continued to ride the Trek.

Fortunately I now ride the light rail early, and there are so few passengers that I no longer need a folding bike in the morning. The Trek is not as compact as a folded Swift, but does fit under my desk. And since I ride home, I don’t have to deal with a crowded train at rush hour.

It has been well over a month since I felt any knee pain at all. I now have the Swift setup with grocery bags for one mile rides to the nearby stores, but ride the old Trek to and from work.