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Category: Health
On genetic privacy
Larry Moran has a post up, Who Owns Your Genome?, where he mentions me apropos of the HeLa genome disclosure:
In my opinion, there is no excuse for publishing this genome sequence without consent.
Razib Khan disagrees. He thinks that he can publish his genome sequence without obtaining consent from anyone else and I assume he feels the same way about the sequence of the HeLa genome [Henrietta Lacks’ genome, and familial consent].
In response to Larry, I don’t have a definitive opinion about the HeLa genome disclosure in terms of whether it was ethical to release it or not. “Both sides” have positions which I see the validity of. I think ultimately the root issues really date to the 1950s, not today, and they don’t have to do with personal genomics as such. Also, I’d recommend Joe Pickrell’s post, Henrietta Lacks’s genome sequence has been publicly available for years.
Larry also has a question in the comments:
Putting a stop on the biological clock
Egg freezing enters clinical mainstream:
Egg freezing is no longer an experimental procedure, according to the American Society for Reproductive Medicine (ASRM), which on 22 October issued new guidelines on the controversial practice. The change in policy is expected to accelerate the growth of clinics that offer egg freezing to women who face fertility-damaging treatment for cancer or other conditions, and to women wishing to delay having a baby — although the society stopped short of endorsing the procedure for that purpose
You can read the full guidelines, with caveats, online. Last I checked this costs on the order of $10,000. Nothing to sneeze at, but definitely not insane when you consider how much money many couples spend on fertility technologies when women are between 35 and 40.
And of course I recommend freezing sperm too. That’s far less costly.
The moral measure of bad teeth
Recently I was at the dentist and I was told that because I did not have any caries at this age, I would probably not have to worry about that in the future (in contrast, I do have some issues with gingivitis). I wasn’t surprised that I didn’t have caries, I have no great love of sweet confections. I had chalked up my evasion of this dental ailment to my behavior. To make a long story short my dentist disabused me of the notion that dental pathologies are purely a function of dental hygiene and diet. Rather, he explained that many of these ailments exhibit strong family and ethnic patterns, and are substantially heritable. My mother did suffer from periodontal disease a few years back, and that has made me much more proactive of my own dental health.
As someone who is quite conscious of the power of genetics, I was quite taken aback by this blind spot. I realized that not only did I attribute my own rather fortunate dental health (so far) to my personal behaviors, but, I had long suspected those with dental issues of less than optimal habits. Obviously environment (e.g., high sugar diet) does matter. But apparently a great deal of the variation in the trait is heritable. If you are still curious, here’s a paper which might interest you, Heritable patterns of tooth decay in the permanent dentition: principal components and factor analyses.
Being fat is like being gay (?)
Anti-obesity: The new homophobia?:
Consider the many parallels between the treatments advocated by those who claim being gay is a disease, and those being pushed by our public health establishment to “cure” fat children and adults of their supposedly pathological state.
The advocates of so-called conversion or reparative therapy believe that “homosexuality” is a curable condition, and that a key to successful treatment is that patients must want to be cured, which is to say they consider same-sex sexual orientation volitional. These beliefs mirror precisely those of the obesity establishment, which claims to offer the means by which fat people who want to choose to stop being fat can successfully make that choice.
Those who seek to cure homosexuality and obesity have tended to react to the failure of their attempts by demanding ever more radical interventions. For example, in the 1950s Edmund Bergler, the most influential psychoanalytical theorist of homosexuality of his era, bullied and berated his clients, violated patient confidentiality and renounced his earlier, more tolerant attitude toward gay people as a form of enabling. Meanwhile, earlier this year a Harvard biology professor declared in a public lecture that Mrs. Obama’s call for voluntary lifestyle changes on the part of the obese constituted an insufficient response to the supposed public health calamity overwhelming the nation, and that the government should legally require fat people to exercise.
The eternal question of calorie restriction
There’s a lot of buzz about a new paper in Nature (yes, I know there’s always buzz about some Nature paper or other), Impact of caloric restriction on health and survival in rhesus monkeys from the NIA study. You’ve probably heard about calorie restriction before. For me the issue I have with it is that people who are very knowledgeable (i.e., researchers who know a great deal abut human physiology, etc.) have given me contradictory assessments of this strategy of life extension. But it’s not totally crazy, there are serious scientists at top-tier universities who practice calorie restriction themselves. This isn’t the final word, but I wouldn’t be surprised if it is going to take decades for it to resolve itself for humans specifically (because some people will always be, and perhaps rightly, extrapolating from short-lived organisms to humans when it comes to modulations of lifespan in the laboratory). The New York Times piece had a really strange coda:
Dr. de Cabo, who says he is overweight, advised people that if they want to try a reduced-calorie diet, they should consult a doctor first. If they can handle such a diet, he said, he believes they would be healthier, but, he said, he does not know if they would live longer.
Some scientists still have faith in the low-calorie diets. Richard Weindruch, a director of the Wisconsin study, said he was “a hopeless caloric-restriction romantic,” but added that he was not very good at restricting his own calories. He said he might start trying harder, though: “I’m only 62. It isn’t too late.”
Then there is Mark Mattson, chief of the laboratory of neurosciences at the National Institute on Aging, who was not part of the monkey study. He believes there is merit to caloric restriction. It can help the brain, he said, as well as make people healthier and probably make them live longer.
Dr. Mattson, who is 5-foot-9 and weighs 130 pounds, skips breakfast and lunch on weekdays and skips breakfast on weekends.
A circumcision compromise?
The New York Times has a piece on an update to the American Academy of Pediatrics position statement on circumcision (shifting toward a more pro-circumcision position of neutrality). In the United States the rates of circumcision for infant boys has gone from 80-90% to ~50% (there are regional variations, so only a minority of boys in the Pacific Northwest are circumcised). A few years ago Jesse Bering put up a post, Is male circumcision a humanitarian act?, where he actually wrote “Nobody knows where your child will live as an adult (perhaps Africa), or how rampant HIV will be there….” I like taking probabilities into account, but this is ridiculous.
Why some people don't think Down Syndrome is bad
I often criticize Lefty readers for their lack of reality-basis. Specifically, they often want to align reality with their own normative preferences, even though normative preferences aren’t necessarily contingent upon reality (e.g., sex differences). My post on Down Syndrome has elicited similar responses, but from people one might term social conservatives. So, for example, Ursula and Matthew Hennessey have taken to denouncing me on Twitter, albeit for statements that they no doubt find extremely objectionable. Not too surprising. But I found this post, A gift named Magdalena, particularly instructive:
But we aren’t victims. In fact, we’re the opposite. We are supremely lucky. Magdalena isn’t sick. Down syndrome is not a disease; it’s merely a collection of traits, all of which occur, though not all at once, in so-called “normal” people.
But how could Down syndrome be a gift? Surely that’s taking it too far. How could a lifetime of likely dependency be a gift? How could impaired cognitive development be a gift? How could gastroesophageal reflux disease and its expensive, twice daily medicine be a gift? How could two full years of potty training with no end in sight be a gift?
The truth is that there is no objective bright line between trait and disease. In fact, nature does not know trait or disease, it only knows phenotypes. Being white skinned in a pre-modern world is a disease at the equator, and being black skinned in Scandinavia would also have been a disease. In theory you could argue that Down Syndrome is not a disease either. The Hennessey’s are correct that the collection of traits of DS individuals can be found elsewhere. So imagine that a chemical exposure or some such thing functionally transformed a child with a normal karyotype into one with Down Syndrome. How would most people feel about this? Would parents view it as a gift?
Who is the decider of the good life?
‘Ashley treatment’ on the rise amid concerns from disability rights groups:
A controversial procedure to limit the growth of severely disabled children to keep them forever small – which ignited a fiery debate about the limits of medical intervention when it was first revealed five years ago – has begun to spread among families in America, Europe and beyond.
…
Five years ago details first emerged of Ashley, a nine-year-old girl living near Seattle. She was born with developmental disabilities that meant she was unable to talk or walk, and continues to have the cognitive ability of an infant.
…
The core of the treatment was hormone therapy: high estrogen doses to bring forward the closure of the growth plates in her bones, which would in turn stop her growing. In addition, surgical interventions included removal of her nascent breast buds to avoid the discomfort of fully-formed breasts later in life, and a hysterectomy to avoid menstruation.
..
Silvia Yee, a lawyer with the Disability Rights Education & Defense Fund that is run jointly by disabled people themselves and parents of children with disabilities, said: “This is what we were fearing. It is becoming just one more choice on the menu of possibilities – a medical operation that will change a person’s life. Who has the right to decide to change an individual into a different entity?“
American medicine & American red-tape
I just attended a presentation where a researcher outlined how epigenomics could help patients with various grave illnesses. Normally I don’t focus on human medical genetics too much because it always depresses me. I don’t understand how medical geneticists don’t start wondering what hidden disease everyone around them has. In any case the researcher outlined how epigenomic information allowed for better treatment, so as to extend the lives of patients. All well and good. But then one individual in the audience began asking pointed questions as to the medical ethics of the enterprise, and whether the researcher had cleared some legally sanctioned hurdles. More specifically, there was a question whether exploring someone’s epigenomic profile might expose private information of their relatives! (because relatives share epigenomic and genomic profiles to some extent)
Frankly I began to get enraged at this point. People are suffering from terminal illnesses, and considerations of the genetic privacy of their near relatives are looming large? Seriously? The reality is that manifestation of a disease itself gives one information about the risks of their relatives. In any case, the researcher admitted that further progress in this area is probably going to be due to the investments of wealthy individuals (e.g., people like Steve Jobs who have illnesses) as well as outside of the United States. You’re #1 America!
Personal genomics: more than fun & games
My main current interest in personal genomics right now is pure recreation. I don’t expect much utility out of it, because a lot of correlations between genes (SNPs, etc. ) and traits/diseases are rather weak. But there are some exceptions. Recently I was temporarily put on a prescription medication and I wanted to check if I was a fast or slow metabolizer. The material you see in the medical literature is that Europeans tend to be slow metabolizers, while Asians tend to be fast metabolizers. Since I’m Asian, I’m probably a fast metabolizer, right? Not so fast! Though I’m geographically Asian (my family hails from Asia), in terms of ancestry South Asians tend to be closer to Europeans, though with some affinity to East Eurasian populations as well. But another issue for me is that I clearly have 10-15% more recent East Asian ancestry, which is not typical in South Asians. In other words, I can’t infer with any confidence from generalizations about Asians and Europeans in the American medical literature to my personal status.
Eugenics as a luxury of the affluent
In the comments below Jason says in regards to the connection between eugenics and genocide and the “slippery slope”:
In your current comfortable first world circumstances, you are right the slope is perhaps not that slippery. I hope you are never tested in a less comfortable setting as then I think you might find it can be pretty slippery after all.
A reference to the interlocutor’s status as a citizen of the comfortable First World (which itself is a somewhat archaic term by now I think) seems de rigueur in many arguments. And I think many people will find it plausible that someone in an affluent consumer society would be blind to the “dark side” of eugenics, and how it could lead to genocide. But I think this plausibility is entirely superficial, and collapses upon closer inspection. Rather, it is I believe in “First World” and advanced nations where the likelihood of the ubiquity of eugenics and possible genocide predicated on systematic eugenics is going to be the most probable outcome.
None dare call it eugenics
In the comments below Phillip Lemky observes:
Hi Razib. I find disturbing all this talk of assortative mating and biological castes, as it sounds eerily similar to eugenics. Please correct me if I’m mistaken to be making this connection.
This is a common response to some of the things mooted on this weblog. Freddie deBoer even sent me a peculiar email last year expressing how appalled he was at some of the topics and comments in these parts (if you know Freddie’s internet reputation, this is not surprising behavior). First, I don’t know what people mean by “eugenics.” Here is the first sentence in Wikipedia for the eugenics entry:
Eugenics is the “applied science or the bio-social movement which advocates the use of practices aimed at improving the genetic composition of a population”, usually referring to human populations….
Wikipedia isn’t authoritative, and colloquial definitions can deviate from “official” definitions. As a rule I don’t generally talk much about state coercion or manipulation of the reproduction of the citizenry, so I don’t see that I’m talking about classical eugenics. But, it does seem that there are eugenical implications in the mass action of human behavior and the flexibility of choices which modern humans have. Consider this long article in The New York Times Magazine, The Two-Minus-One Pregnancy:
Pleasure through signalling
As some of you know, I have a problem. An addiction that is. For most of the year I stock up on fresh habanero pepper. Usually I try to limit myself to 1-2 peppers per meal…but when not in the company of others who may civilize me I can lose control and eat more than half a dozen in a sitting. After the first few peppers they just don’t taste as spicy, and I suppose psychologically I am under the illusion that enough peppers will bring back the pleasure high of a few moments earlier. I developed this habit not through cultural inculcation. Rather, when I went off to college and no one supervised me I began to eat more and more peppers, and developed an extremely high threshold of tolerance. By the end of college I began to raid my parents’ thai peppers at home to the point where they complained that I always left their stock depleted before going back to school. At this point I can drink tabasco sauce like gatorade.
But the different parts of the gastrointestinal system adapt differently. When I “habanero gorge” I develop extreme pain in my bowels in a few hours, and of course there are issues the next day. Over the years I’ve poked around the literature on possible correlations between pepper consumption and stomach cancer, or the anti-pathogenic properties of peppers. I’m pretty sure I’m well beyond the limit of normal consumption in any of these studies.
My primary motivation in consuming peppers is pure hedonism, as can be attested by the fact that my consumption is constrained by the presence of others. But there are clear social consequences to eating extremely spicy food. People take notice when you pile on crushed read peppers onto pizza, or pull out a habanero at In-N-Out Burger. At nice restaurants you sometimes get well known for being the guy who likes the habanero paste lathered onto his beef, to the point where new servers might drop by to gawk. There can be a clear element of social signalling in consuming very spicy foods. In short, people can think you are a “badass.” Of course actually I’m a cheerful and self-effacing individual! (granted, with a casual tendency to verbally bludgeon people)
1 out of 3 young Iranian men "gay"?
Married at age 21
A few years ago the president of Iran, Mahmoud Ahmadinejad, asserted that his nation did not have gays as they did in the West. What Ahmadinejad seems to have meant is that a public gay identity does not exist in Iran. He has to be aware that homosexual behavior is not unknown in his nation. More generally Ahmadinejad’s comments brought up the issue of men having sex with men throughout the Middle East before marriage. This is a taboo topic in much of the region, so getting good quantitative data seems pretty much impossible. But today PLoS Medicine came out with a paper with a result which suggests that the anecdotes of relatively widespread homosexual behavior in the Middle East are not totally unfounded or unrepresentative (the journalist Hugh Pope has indicated that Middle Eastern men have sometimes assumed he would naturally be open to sexual propositions because he was a Westerner. He grew a mustache to discourage such inquiries) . The paper is about HIV, Are HIV Epidemics among Men Who Have Sex with Men Emerging in the Middle East and North Africa?: A Systematic Review and Data Synthesis. Here’s the figure which jumped out at me:
Probability of pregnancy by age
I just finished reading My Fertility Crisis, which is excerpted from a longer piece you can get on Kindle for $1.99. The author is a single woman in her early 40s who is going through IVF treatments, without success so far. She outlines the choices she made over her life which may have influenced her current situation.
After reading the piece I came back to an issue I’ve wrestled with before: it’s often really hard to find information on probability of pregnancy online in the form of charts. The reason is that there’s so much information, and much of it is skewed toward people who are undergoing treatment for infertility. But why look when you can generate your own visualization? I found a pregnancy probability calculator online which I cross-validated with some of the literature. Here is the best case scenario for probability of pregnancy if you are trying in the natural fashion (the probabilities exclude women who are clinically infertile, which is a rather slippery category strongly dependent on age, so the older cohorts are probably much larger overestimates than the younger ones):
The main focus is really the decade of the 30s for women. Here is a figure from Ovarian Aging: Mechanisms and Clinical Consequences which shows a finer-grain decline in fertility:
Dominance, the social construct that confuses
A story in The Los Angeles Times seems to point medical implications of being a sickle cell carrier, Sickle cell trait: The silent killer:
At least 17 high school and college athletes’ deaths have been tied to sickle cell trait during the past 11 years. The group includes Olivier Louis, a player at Wekiva High School near Orlando, who died on Sept. 7, 2010, following his first football practice.
You have surely heard about sickle cell anemia. It is a recessive disease which expresses in those who carry two sickle cell alleles. T-boz of TLC has the disease for example due to her homozygosity. But the allele also famously confers some resistance against malaria, which explains its concentration in regions which have historically been malarial. Sickle cell is arguable the classic case of heterozygote advantage driving the emergence of a recessive disease. The frequency of the allele is balanced at the equipoise between the proportion of people who are more susceptible to malaria if its proportion is too low and those who express sickle cell anemia if its proportion is too high. This advantage is obviously context sensitive. The standard assumption is that in a non-malarial environment selection pressure against anemia will drive the frequency of the allele down over time as heterozygotes don’t impose a floor in the proportion of the mutant allele. This seems to have occurred among African Americans, they’re ~80% West African, but their frequency of the sickle cell anemia allele is less than {0.80*(the West African proportion)} from what I know (remember that the median number of generations which an African American’s black ancestors have been in the USA is probably ~10).
Marry far and breed tall strong sons
The Pith: When it comes to the final outcome of a largely biologically specified trait like human height it looks as if it isn’t just the genes your parents give you that matters. Rather, the relationship of their genes also counts. The more dissimilar they are genetically, the taller you are likely to be (all things equal).
Dienekes points me to an interesting new paper in the American Journal of Physical Anthropology, Isolation by distance between spouses and its effect on children’s growth in height. The results are rather straightforward: the greater the distance between the origin of one’s parents, the taller one is likely to be, especially in the case of males. These findings were robust even after controlling for confounds such as socioeconomic status. Their explanation? Heterosis, whether through heterozygote advantage or the masking of recessive deleterious alleles.
The paper is short and sweet, but first one has to keep in mind the long history of this sort of research in the murky domain of human quantitative genetics. This is not a straight-forward molecular genetic paper where there’s a laser-like focus on one locus, and the mechanistic issues are clear and distinct. We are talking about a quantitative continuous trait, height, and how it varies within the population. We are also using geographical distance as a proxy for genetic distance. Finally, when it comes to the parameters affecting these quantitative traits there are a host of confounds, some of which are addressed in this paper. In other words, there’s no simple solution to the fact that nature can be quite the tangle, more so in some cases than others.
Because of the necessity for subtlety in this sort of statistical genetic work one must always be careful about taking results at face value. From what I can gather the history of topics such as heterosis in human genetics is always fraught with normative import. The founder of Cold Spring Harbor Laboratory, Charles Davenport, studied the outcomes of individuals who were a product of varied matings in relation to genetic distance in the early 1920s. This was summed up in his book Race Crossing in Jamaica:
A quantitative study of 3 groups of agricultural Jamaican adults: Blacks, Whites, and hybrids between them; also of several hundred children at all developmental stages. The studies are morphological, physiological, psychological, developmental and eugenical. The variability of each race and sex in respect to each bodily dimension and many basis vary just as morphological traits do. In some sensory tests the Blacks are superior to Whites; in some intellectual tests the reverse is found. A portion of the hybrids are mentally inferior to the Blacks. The negro child has, apparently, from birth on, different physical proportions than the white child.
Good calories, bad potatoes?
Changes in Diet and Lifestyle and Long-Term Weight Gain in Women and Men:
Within each 4-year period, participants gained an average of 3.35 lb (5th to 95th percentile, −4.1 to 12.4). On the basis of increased daily servings of individual dietary components, 4-year weight change was most strongly associated with the intake of potato chips (1.69 lb), potatoes (1.28 lb), sugar-sweetened beverages (1.00 lb), unprocessed red meats (0.95 lb), and processed meats (0.93 lb) and was inversely associated with the intake of vegetables (−0.22 lb), whole grains (−0.37 lb), fruits (−0.49 lb), nuts (−0.57 lb), and yogurt (−0.82 lb) (P≤0.005 for each comparison). Aggregate dietary changes were associated with substantial differences in weight change (3.93 lb across quintiles of dietary change). Other lifestyle factors were also independently associated with weight change (P<0.001), including physical activity (−1.76 lb across quintiles); alcohol use (0.41 lb per drink per day), smoking (new quitters, 5.17 lb; former smokers, 0.14 lb), sleep (more weight gain with <6 or >8 hours of sleep), and television watching (0.31 lb per hour per day).
I took the results when they controlled for other variables and filtered them all so that their p-values were 0.001 or less (in fact, of the ones below only “sweets and desserts” is p-value 0.001, all the others are below that). Nothing too surprising, but the magnitude of effect of french fries was pretty large:
Less fear of the flu for asthmatics?
One of the reasons I tend toward a bit of hypochondria is probably the fact that what for others are inconvenient minor ailments often trigger my asthma. So nice to see this, Why Does Flu Trigger Asthma?:
When children with asthma get the flu, they often land in the hospital gasping for air. Researchers at Children’s Hospital Boston have found a previously unknown biological pathway explaining why influenza induces asthma attacks. Studies in a mouse model, published online May 29 by the journal Nature Immunology, reveal that influenza activates a newly recognized group of immune cells called natural helper cells — presenting a completely new set of drug targets for asthma.
If activation of these cells, or their asthma-inducing secretions, could be blocked, asthmatic children could be more effectively protected when they get the flu and possibly other viral infections, says senior investigator Dale Umetsu, MD, PhD, of Children’s Division of Immunology.
Although most asthma is allergic in nature, attacks triggered by viral infection tend to be what put children in the hospital, reflecting the fact that this type of asthma isn’t well controlled by existing drugs.
For various reasons I’m moderately skeptical of incremental improvements in life expectancy in developed nations through drugs. But, I do think there are plenty of possibilities when it comes to reducing morbidity, and therefore increasing productivity of a life well lived.
Kissing and cancer
I recently listened to Paul Ewald talk about how a lot of cancer is due to infection on the radio show To the Best of Our Knowledge. That wasn’t too surprising, Ewald has been making the case for a connection between infection and lots of diseases for a while. What jumped out at me is his claim that kissing can spread some of the viruses. Here’s something he told Discover a few years back:
D: How do we get infected with these dangerous pathogens?
PE: Two of the most powerful examples are sexual transmission and kissing transmission, and by that I mean juicy kissing, not just a peck on the cheek. If you think about these modes of transmission, in which it might be a decade before a person has another partner, you realize that rapidly replicating is not very valuable—the winning strategy for the microbe would be to keep a low profile, requiring persistent infections for years. So we would expect that disproportionately, the sexually transmitted pathogens would be involved in causing cancer, or chronic diseases in general. You can test this. Just look at the pathogens that are accepted as causing cancer—Epstein-Barr virus, Kaposi’s sarcoma–associated herpesvirus, human T lymphotropic virus 1—and find out whether they’re transmitted this way. They almost all are. A random sample would yield maybe 15 to 20 percent of pathogens associated with cancer being sexually transmitted, yet the figure is almost 100 percent. When you look at viruses alone, it is 100 percent.
If a lot of kissing and number of sexual partners is predictive of risk of cancer, my immediate thought is that this naturally explains a lot of the cancer that runs in families. Families can pass on genes and cultural norms which would favor or disfavor certain behaviors.
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Razib’s Pinboard
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- Liberals for Low Wages | The American Conservative
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- Brain drain to Wall Street: Goldman Sachs hires ‘God particle’ physicist | AEIdeas
- mathbionerd: My breasts. My genes.
- Washington Post
- The Court Case Looming Behind Angelina Jolie's Breast Cancer Column - Andrew Cohen - The Atlantic
- Boys Killed Pets to Become Warriors in Early Russia
- The genomics of selection in dogs and the parallel evolution between dogs and humans : Nature Communications : Nature Publishing Group
