Recently in Biology Category


February 14, 2010

OK, so I thought that the Dyson Blade dryer was scary, but check this out: gas plasma-based hand sanitizers.
Plasmas engineered to zap microorganisms aren't new. During the last decade, they have come into use to sterilize some medical instruments. But using them on human tissue is another matter, said Mark Kushner, director of the Michigan Institute for Plasma Science and Engineering and a professor at the University of Michigan in Ann Arbor. "Many thousands of volts drive the generation of plasma," he said, "and normally one doesn't want to touch thousands of volts." But the design of the new hand sanitizers, he said, protects people from doing so. Reassured by that design, about five years ago he put his naked thumb into a jet of microbe-destroying plasma at the lab of another plasma researcher.


The plasma cleaners make their antibacterial cocktails by running electrical current through air, said David B. Graves, a professor of chemical engineering at the University of California, Berkeley, who has worked on low-temperature plasma applications for 25 years.

Professor Graves is doing computer simulations of the chemical reactions that occur in the Morfill plasmas. The electric current ionizes the oxygen, nitrogen and water vapor in the air, he said, eventually creating the nitric oxide, hydrogen peroxide and particles that are so effective against bacteria, viruses and fungi.

OK, so I'm sold that it probably won't burn my hand off, but that doesn't necessarily mean that it's something I want to expose my hands to. Nitric oxide, for instance, is not very good for you:

Nitric oxide vapors are a strong irritant to the pulmonary tract. At high concentrations initial symptoms of inhalation may be moderate and include irritation to the throat, tightness of the chest, headache, nausea and gradual loss of strength. Severe symptoms may be delayed (possible for several hours) and include cyanosis, increased difficulty in breathing, irregular respiration, lassitude and possible eventual death due to pulmonary edema in untreated cases.

That sure sounds like fun!

Seriously, the relevant question here is how wide the difference is between the level at which the relevant chemicals deactivate bacteria, viruses, etc. and the level at which they cause side effects in humans. If there's a wide gap, then great, but if not, then we have to worrry about how well the plasma generator is calibrated. In addition, there's the question of the effect of regular exposure (e.g., for health care workers). I'll be interested to see what safety studies show.


December 31, 2009

I'm probably late to the party here but I wanted to make note of the NYT's recent article on water safety. (þ Melanie Schoenberg). While there's certainly some stuff here one might be distressed about, the article is written in such a way that it's pretty hard to evaluate how serious the issue actually is.

The article seems to make three major factual claims:

  • The Safe Water Drinking Act only regulates a small fraction of the potentially hazardous chemicals potentially found in drinking water.
  • Many municipal water systems contain chemicals at levels which, while legal, may be unsafe (e.g., are above EPA safe levels).
  • People are getting sick from this.
I don't doubt that the first of these is true: according to the article, 60,000 plus chemicals are used within the US (I'm actually surprised it's this low, since the PDR has over 4000 drugs and MSDS.COM claims to have 3.5 million data sheets), and it's not clear how you would plausibly analyze all of these, let alone determine permissible levels for each of these. I'm not saying this is desirable, but it's not necessarily a disaster either. Ultimately, you can either have an "default accept" or "default deny" policy here; given how sensitive modern analytic techniques are, if your policy is "default deny" you're going to spend a lot of time removing trace concentrations of harmless chemicals from your water supply. On the other hand if it's "default accept" you're going to end up with a lot of chemicals in your water that you don't really know are safe.

Given the first point, the second isn't surprising either. With that said, I'm not sure that the Times is really representing the situation that accurately. For instance, here's the report for Palo Alto, where I live. The Times reports "1 contaminant below legal limits, but above health guidelines", with the contaminant being alpha particle activity at a mean rate of 4.56 pCi/L. Let's see if we can put this in perspective. Assume humans are made entirely of water and rescale into kg, so we have 4e-12 Ci/kg of human body mass. A Ci is 37e+9 disintegrations/s so multiplying out we have .148 disintegrations/kg/s. If we assume that all the alpha particles are from U-238, and the alpha particles are being emitted at 4.270 MeV (~ 7e-13 J), then we get 1e-13 J/kg/s. If we assume that all of these are absorbed (not crazy since alpha particles have a very short path in the body) then we're getting 1e-13 Grays/s or 2e-12 Sv/s (multiply by the 20 Q factor for alpha particles) or .03 mSv/year. For comparison, the background level of radiation is 2.4 mSv/year. Obviously this isn't something you should be that thrilled about, but it's not clear to me that a 1% increase in your radiation dose is that bad either.

Given that, why does the NYT list this as above the health level? The answer seems to be that their safe value for alpha particles is zero (the legal limit is 15 pCi/L): the maximum level of alpha particle activity in neighboring Mountain View is 2.56 pCi/L, but it's still listed as having 5 "above health" samples (Chicago had one reading of .88 pCi/L and is also listed as a positive). This all makes me wonder if something is wrong here and the NYT is showing false positives. Of course, when you're processing a lot of data it's easy to make mistakes—assuming this is a mistake. It could be that I'm confused or that it's just the alpha particle threshold that's too low. I e-mailed the times to ask them for a copy of the raw data, but I haven't heard anything yet.

This brings us to the final point: the Times writes:

All told, more than 62 million Americans have been exposed since 2004 to drinking water that did not meet at least one commonly used government health guideline intended to help protect people from cancer or serious disease, according to an analysis by The Times of more than 19 million drinking-water test results from the District of Columbia and the 45 states that made data available.


And independent studies in such journals as Reviews of Environmental Contamination and Toxicology; Environmental Health Perspectives; American Journal of Public Health; and Archives of Environmental and Occupational Health, as well as reports published by the National Academy of Sciences, suggest that millions of Americans become sick each year from drinking contaminated water, with maladies from upset stomachs to cancer and birth defects.

This seems to conflate a bunch of issues. There seems to be a lot of variance in the data, with some tests showing positive results and some negative results (or low levels) for the same toxin even in the same area. It's very different to drink water with a toxin in it once than it is to drink it ever day for 10 years. I spent a couple days in Boston in 2007, but I'm not overly concerned about the fact that I might have been exposed to twice the legal limit of haloacetic acids in the two to four liters of water I drank while I was there. More generally, while one positive test may qualify as an exposure, it's not clear what that means as far as the real level of risk people are incurring. And of course there's a difference between cumulative toxins (e.g., arsenic) and acute toxins (e.g., e. coli). Speaking of e. coli, "maladies from upset stomachs to cancer and birth defects" covers a lot of territory; it's one thing if a sewer system occasionally fails to remove all the bacteria from the water supply (not that that's good) and another if it delivers hot and cold running cyanide from the tap.

Obviously, when you read this article you're supposed to be scared, but the way the article is written (and the opaque data presentation) doesn't make me feel like I have enough data to know if I should be or not.

P.S. San Francisco really does have great water. Almost good enough to make up for destroying Hetch Hetchy..


November 29, 2009

I'd been mostly avoiding developing an opinion on the H1N1 pandemic, but I recently had someone ask me about it and then watched this ABC reportCogitamus) and figured it might be time to read some of the literature. Your go-to site here for statistics is CDC FluView (the above report complains about availability, but I don't think anyone is claiming that CDC is actually misreporting the data). After reading through CDC's data, the situation seems to be as follows:
  • We're seeing over twice as much "influenza-like illness" (ILI) as normal this year (5.5% of visits versus 2.3% of visits).
  • When tested, the majority of these cases (70+%) aren't actually flu.
  • The vast majority of cases that are actually flu are H1N1.
  • Mortality from pneumonia and influenza is currently at 7.5%, what looks like about 50-75% over the seasonal baseline and over the 6.9% epidemic threshold. So, you're looking at like a 2.5% excess risk of death. This doesn't sound too bad for adults.
  • We're seeing something like 2x ordinary pediatric mortality: 20 deaths in the week Nov 7-14, 138 deaths since August 30 and 200 since April 30. It's difficult to compare here since the CDCs ordinarily mortality data is broken up into different cohorts. Ordinarily there are around 10,000 deaths in the US in 2006 in the 1-14 cohort and 35,000 in the 15-24 cohort [*]. It we crudely divide by 52, we get something like 200 deaths/week in the 1-14 cohort and maybe something like 400 deaths/week in the the 1-17 cohort (assuming its evenly distributed in the 15-24 range). So, this year's flu represents somewhere around 2-10% excess mortality over usual, which doesn't sound that bad.
  • It looks like the rate of flu is coming down both in the US and Canada. The Canadians say they may have reached their "epidemic peak".
  • Quebec appears to be plague central, with the highest rate of hospitalizations of any province in Canada.

I'm most struck by how high a fraction of people with disease suspicious enough to be tested actually turn out not to have flu. This isn't just a case of US health care overtreatment, either, The Canadian positive rate is a little over 40%. That said, the rate of positives varies really dramatically from region to region, with a low of 13.3% in region 6 (AR, LA, NM, OK, TX) and a high of 51.8 in Region 3 (DE, DC, MD, PA, VA, WV), but it's hard to tell (or rather I'm too lazy to run the numbers) if it's just a matter of basic incidence or of the amount of testing being done.

One question people seem to want to ask is: should I get the vaccine? I know there are concerns about side effects, though as far as I can tell, there isn't much to be worried about (you can find the CDC party line here and Wikipedia's rundown here): the US versions of the H1N1 vaccine seem to be made with the same methods as the seasonal vaccine, so if you were happy to get that, you should be OK with the H1N1 vaccine too. [There have been concerns about the vaccines used outside the US which contain adjuvants, and I haven't developed an opinion on that.].

As far as effectiveness goes, the studies that are available seem to use the stimulation of an immune response rather than actually getting H1N1 as a study endpoint. This is understandable, since randomized controlled trials with infection as the endpoint are slower and more expensive to do, but it makes the data less useful for decision making than it otherwise would be. This Atlantic article argues that the overall evidence for flu effectiveness is thin, but compare this CDC survey which seems to indicate effectiveness in the 55-85% range. Anyway, if we assume that your chance of getting the flu is 5-20% and everyone gets vaccinated, then we'll see something like a 3.5-15% reduction in disease cases (number to treat = 6-30). On the other hand, since apparently most cases of ILu aren't actually flu, the improvement in your chance of experiencing some sort of flu-like crud (which is after all what you care about) are only like 1-5%, ignoring, of course, that flu season seems to be mostly over now.


April 23, 2009

OK, so this is pretty clever:
Biological molecules exhibit homochirality and are optically active. Therefore, it is possible that the scattering of light by biological molecules might result in a macroscopic signature in the form of circular polarization. If this is the case, then circular polarization spectroscopy, which may be utilized in remote sensing, can offer a powerful indicator of the presence of a universal biosignature, namely homochirality. Here, we describe laboratory experiments designed to investigate this idea. We focus on photosynthetic microorganisms, and also show results from macroscopic vegetation and control minerals. In the microorganisms, we find unambiguous circular polarization associated with electronic absorption bands of the photosynthetic apparatus. Macroscopic vegetation yields a stronger and more complex signature while the control minerals produce low-levels of circular polarization unrelated to their spectra. We propose a heuristic explanation of our results, which is that the polarization is produced by circular dichroism in the material after the light has undergone its last scattering event. The results are encouraging for the use of circular polarization spectroscopy in remote sensing of a generic biomarker from space or the ground.

Writeup here. I don't know if it will work, but clever...


April 20, 2009

Look if John Boehner wants to believe that global warming isn't happening or isn't bad or whatever, then fine. But can we at least be spared this kind of stupidity:
STEPHANOPOULOS: So what is the responsible way? That's my question. What is the Republican plan to deal with carbon emissions, which every major scientific organization has said is contributing to climate change?

BOEHNER: George, the idea that carbon dioxide is a carcinogen that is harmful to our environment is almost comical. Every time we exhale, we exhale carbon dioxide. Every cow in the world, you know, when they do what they do, you've got more carbon dioxide. And so I think it's clear...

OK, so this is, as Wolfgang Pauli is supposed to have said "not even wrong". First, nobody is claiming that CO2 is a carcinogen. The reason people want to reduce CO2 emissions isn't that they give you cancer, it's that CO2 causes global warming. So, the fact that you exhale it hardly leads to the conclusion that it's somehow a great idea to radically increase the CO2 content of the atmosphere.

Even if the reason to restrict CO2 was that it was bad for humans instead of the environment (like, say mercury) this wouldn't follow. Have you noticed that you're inhaling CO2? It's a waste product from aerobic respiration (look up the Krebs Cycle). Boehner's argument is like suggesting that feces isn't bad for you because you emit it regularly, as do cows, etc., but I'm assuming he'd like to minimize his feces consumption.

Interestingly, while CO2 is a waste product, it's not actually toxic. You wouldn't want to breathe an all CO2 atmosphere, but CO2 is what stimulates the breathing reflex. Oxygen, on the other hand, is fairly toxic once you get too far above the normal partial pressures in the atmosphere.


March 16, 2009

Perry Metzger (via Mangan's and Patri Friedman) points me to this paper on the impact of Vitamin C on endurance training. The basic result is that Vitamin C supplementation in rats seems to significantly decrease the effect of endurance training. The hypothesized (though they have expression studies to back it up) mechanism is that the production of free radicals during exercise stimulates mitochondrial development in the muscle and that taking antioxidants interferes with this mechanism, resulting in a reduced training effect: there isn't a significant impact on VO2max, but rats treated with training along will run significantly longer than those treated with training plus vitamin C (where the test is a forced treadmill run with shock as incentive.) The authors also did a small human study, and the vitamin C group performs worse but the results aren't statistically significant.

Some initial thoughts:

  • Obviously, it would be nice to see a bigger trial on humans.
  • The study was done on untrained rats and humans. It would be interesting to see a similar study with trained athletes to see if there is any difference.
  • One of the reasons that athletes tend to supplement with C is on the theory that it improves immune function. Getting sick even once has a huge impact on your training cycle. I don't think the data on immune function is really that convincing, but to the extent to which C does prevent you getting sick, you would need to balance that against the impact on training.
  • If C inhibits the training effect, what impact does it have in the post-training period? Is there an argument for some sort of vitamin C cycling?

All that said, I recently ran out of vitamin C and this is making me rethink, at least a little, whether I want to buy more.


February 19, 2009

In Slate this week we're treated to William Saletan's usual handwringing about how biotech, though of course inevitable, inevitably cheapens people's attitudes towards reproduction. This time the issue is preimplantation genetic diagnosis (PGD), where you you do in vitro fertilization and biopsy the embryos to decide which, if any to implant. Obviously, this is something you might want to if you know you're a carrier for something nasty (e.g., Tay-Sachs) and want to avoid passing it on. Saletan's objection, predictably, is that people will use it for purposes he doesn't approve of (sex selection, height selection, etc.):
Two months ago, the Fertility Institutes, an assisted reproduction company headquartered in Los Angeles, began advertising the "pending availability" of genetic tests that would offer "a preselected choice of gender, eye color, hair color and complexion" in artificially conceived children. On Thursday, Gautam Naik of the Wall Street Journal reported that "half a dozen" potential clients had contacted the company to request such tests. As of today, the tests still aren't for sale. But several trends are converging to make aesthetic trait selection an impending business.


See how smooth the transition can be? You're already screening for diseases. Why not add one more factor while you're at it? So now you'll know which embryos are male and which are female, just in case two of them turn out to be healthy and you're lucky enough to be able to choose which one to put in the womb. And if you're checking sex, why not throw in eye color and complexion? You don't have to do anything with the information yet. Just run the test and find out what your options are.


This is how revolutions happen: Technology matures, trends converge, and cultural changes pave the way. By the time Steinberg opens his trait-selection business and does for that practice what he's already doing for sex selection, it'll be too late to stop him. In fact, before you know it, we'll be used to it.

Unfortunately (or fortunately, depending on your perspective), the statistics pretty severely limit the use of for trait selection. The problem is that this is a screening procedure: you don't get to make the embryos you want, you just make a bunch of random embryos and then screen out the ones you don't like. And while any given trait may be reasonably probable, they're not that jointly probable.

In case you've forgotten your high school genetics, there are a bunch of common cases with different probabilities of the embryo expressing the trait:

  • Autosomal recessive traits (ones where you need to have two copies of the allele to show the trait) [blue eyes, Tay-Sachs] but both parents are heterozygous (has one copy). In this case, 1/4 of the candidate embryos will express the trait.
  • Autosomal recessive traits where one parent is homozygous and one is heterozygous. In this case, 1/2 of the candidate embryos will express the trait.
  • Autosomal dominant traits [brown eyes, Huntington's] where both parents are heterozygous, in which case 3/4 of the embryos will express the trait.
  • Autosomal dominant traits where one parent is heterozygous, in which case 1/2 of the embryos will express the trait.
  • Sex-linked traits (e.g., hemophilia), where you express the trait if you have two X chromosomes with the allele (i.e., a homozygous female) or be XY with two the X chromosome having the allele. The statistics vary here based on the father's status and whether the mother is homozygous.

Anyway, to a first order you can think of the chances of getting any particular set of alleles as statistically independent. So, if for instance the father is heterozygous for blue eyes and a Tay Sachs carrier, then there's 1/4 chance each of having: blue/Tay-Sachs, brown/Tay-Sachs, blue/normal, and brown/normal. This creates a real problem for a screening procedure: if you want to select for five traits, each of which have a 1/2 chance of being expressed in the embryo, then any individual embryo has only a 2-5 (1/32) chance of exhibiting the trait. A single egg harvesting yields somewhere in the order of 10-30 eggs [*], so even if all of these turn into good quality embryos, you have somewhere between a 30-60% chance of getting even one embryo with the mix of traits you want. Even if you're willing to go with only three traits, your chances of getting one or more matching embryos is only about 70%. And of course if you're doing IVF and PGD (Did I mention it's horrifically expensive?) so you can screen out some trait, you're already down to somewhere between 1/4-3/4 of embryos before you start screening for height, eye color, etc.


December 25, 2008

One question a lot of athletes have is whether they can work out when they're sick. Obviously, you don't want to lose training time, but on the other hand you don't want to make yourself too sick by training when you should be resting. The conventional wisdom is the "neck" rule (see for instance this article): if your symptoms are above the neck then you can train; if they're below the neck you can't:
David Nieman, Ph.D., who heads the Human Performance Laboratory at Appalachian State University, and has run 58 marathons and ultras, uses the "neck rule." Symptoms below the neck (chest cold, bronchial infection, body ache) require time off, while symptoms above the neck (runny nose, stuffiness, sneezing) don't pose a risk to runners continuing workouts.

This view is supported by research done at Ball State University by Tom Weidner, Ph.D., director of athletic training research. In one study, Weidner took two groups of 30 runners each and inoculated them with the common cold. One group ran 30 to 40 minutes every day for a week. The other group was sedentary. According to Weidner, "the two groups didn't differ in the length or severity of their colds." In another study, he found that running with a cold didn't compromise performance. He concluded that running with a head cold--as long as you don't push beyond accustomed workouts--is beneficial in maintaining fitness and psychological well-being.

The relevant paper is here. Most of the people I know tend to stick to easy distance and avoid hard workouts like intervals. I don't know of any science supporting this theory, though.

This NYT article, sent to me by Eu-Jin Goh, also describes another study that indicates that colds don't impair exercise performance:

The studies began, said Leonard Kaminsky, an exercise physiologist at Ball State University, when a trainer at the university, Thomas Weidner, wondered what he should tell athletes when they got colds.

The first question was: Does a cold affect your ability to exercise? To address that, the researchers recruited 24 men and 21 women ages 18 to 29 and of varying levels of fitness who agreed to be deliberately infected with a rhinovirus, which is responsible for about a third of all colds. Another group of 10 young men and women served as controls; they were not infected.

At the start of the study, the investigators tested all of the subjects, assessing their lung functions and exercise capacity. Then a cold virus was dropped into the noses of 45 of the subjects, and all caught head colds. Two days later, when their cold symptoms were at their worst, the subjects exercised by running on treadmills at moderate and intense levels. The researchers reported that having a cold had no effect on either lung function or exercise capacity.

This actually is a fairly surprising result. Most athletes certainly feel their performance suffers when they're sick. I certainly feel worse training when sick, and while I haven't taken any measurements of lung capacity, I do notice that my heart rate is significantly higher. If anyone has access to the original paper, I'd be very interested in reading it. (Abstract here). Initial impressions: the sample size is pretty small. I'd be interested in seeing a crossover study. What about performance at strength exercises?


December 24, 2008

I recently read Hanna Rosin's piece in The Atlantic about transgender children. The subjects of the piece are children who, from a very young age (< 5) insist that they are—or want to be—the other gender. Even for parents who are basically cool with the concept of the transgendered, this seems to still require some pretty difficult decisions. My take home points from the article go something like this:
  • The current state of sex reassignment (yes, I know that some trans-people prefer the term "gender confirmation surgery", but as far as I know, sex reassignment is still the standard term) technology isn't that great. Certainly, a post-treatment female (i.e., someone who was born male) isn't as much like a biological female as you would like.
  • Sex reassignment treatment works a lot better if you haven't gone through puberty yet.
  • It seems fairly problematic to let children this yound make judgements about something as irreversible as having their genitals reconstructed. Moreover, according to this Endocrine Society review, a significant fraction of children diagnosed with Gender Identity Disorder (GID) experience spontaneous remission post-puberty.
  • There are treatments available which will block/delay puberty, so at least the children are old enough to have a better chance of making their own decisions, though if it's puberty itself that realigns the child's psychological identity with their biological identity, it's not clear that helps as much as you would like. Anyway, if that happens, you can just stop the hormone blockers and let puberty proceed normally.
  • The children in question seem much happier when they're allowed to dress and act as the gender they want to be.
  • There are some psychological treatments which may (or may not) increase the chance that the child will become happier with their biological identity, but they sound pretty uncool (e.g., encouraging extreme traditional gender roles), and after reading the Atlantic article, I came away with the impression that the treated children weren't that happy as adults. But this seems inconsistent with letting them assume their desired gender roles in the interim.

One more note: some of the children in this article seem to have adopted stereotypical opposite sex behaviors incredibly early (like 2-3 years old.) I don't know what that tells us about how preferences for such behaviors get determined, but it's interesting.


December 5, 2008

The Times reports that H.M., a name familiar to generations of psych undergrads, has died. H.M. was a patient who underwent surgical treatment for a seizure disorder which left him unable to form new memories (think Memento but without the tattoos and the ultraviolence.) This made him a popular subject for the study of memory. One of the most interesting features of H.M.'s condition was that he could learn some new physical skills without being conscious of it. When presented with the task he would claim never to have tried it before, but would be able to perform them anyway. The Wikipedia article and the Times obit both make good reading.