About that GMO feeding study in rats... yes, THAT one

Ever since it was published, I'd been wanting to do a takedown of Gilles-Eric Seralini's much-discussed paper finding that rats fed Monsanto's Roundup corn developed tumors at a greater rate than a control group of rats fed non-GMO (genetically modified organism) corn. It turns out I don't really need to write my own article, since plenty of people have done a great job of writing it for me. I really liked this one from the LA Times by Michael Hiltzik.

I'm going to do some choice copy and pasting here:

The research in question is a paper published a few weeks ago by a team led by French biologist Gilles-Eric Seralini. Its findings were explosive: Laboratory rats fed for up to two years on genetically modified corn of a type widely used in the U.S. developed huge, grotesque tumors.

The paper claimed to be "the first detailed documentation of long-term deleterious effects arising from the consumption" of the corn. Seralini found very similar effects in rats fed high dosages of Roundup, a widely used pesticide that the corn had been engineered to tolerate, and in rats fed a combination of the corn and Roundup.

Holy crap, one might rightly think. That's terrifying. But remember that thing I wrote about a few weeks ago about how something being published doesn't necessarily mean it's correct, true, or backed by good science, and that's why we need more double-checking of our colleagues' work? Unfortunately, Seralini's paper is so obviously flawed that even a grad student like myself could pick out mistakes, and I'm astonished it was published at all. For one thing, even the way that it is being billed as some kind of vanguard study, for the first time observing the effects of GMOs in the diet, is entirely false (emphasis mine):

By the way, Seralini's paper isn't the first long-term study of genetically modified foods in the American diet, by a long shot. The same journal that published Seralini's paper (Food and Chemical Toxicology) published a survey of 12 studies of genetically modified corn, soybeans and rice tested on rats, cows, salmon or monkeys for up to two years, and in general found no evidence of any health hazards.

So in stark contrast to the fantastical findings in Seralini's paper, twelve other studies in other animals over the same duration found nothing, and that's just in one journal. This is an anti-GMO argument I see a lot -- for some reason there is this idea that there isn't research being done on the effects of GMOs. I don't know where people are getting this information, because there are tons of studies, both past and present, that mostly show nothing. Seralini's is an astonishing exception.

But okay. Let's not just dismiss it based in it being a lone voice of opposition against a stack of contrasting evidence; after all, sometimes you only need one iconoclast to drastically alter knowledge. Hiltzik nicely broke down the issues with the paper itself:

Among the most common critiques of the experiment is that Seralini used an insufficient number of control rats — 180 test rats were fed genetically modified corn, Roundup or both, but only 20 control rats were fed a purportedly normal diet. Critics say that's too small a control group to be statistically valid.

Of course you'll see more tumor growth in a group that's nine times as large as another group. The proportions are so off that the scientific community dismisses even percentage-based differences between the two groups, because those differences will be more likely to be due to chance. In fact, I could find no evidence in the paper that the authors even tested for statistical significance in the mortality and instances of tumor development between groups. This is a huge -- HUGE! -- red flag. They use misleading statements like "In the female cohorts, there were 2–3 times more deaths in all treated groups compared to controls by the end of the experiment and earlier in general." Announcing from which group rats died earlier is a completely meaningless statement when one group has 180 possible rats that can die and another group only has 20; furthermore, the phrase "2-3 times more deaths" is a tricky phrase because it sounds bad, but it actually only indicates quantity. Saying "2-3 times as likely to die" would indicate tested  -- and (hopefully) verified by statistical significance -- increased odds of death, but "2-3 times more deaths" only means 2-3 times as many rats died in the treatment groups than the control groups, which is again a big DUH since 180 rats vs. 20 rats, well -- you get the picture.

Moreover, the researchers identified no dose-related response: The rats fed higher doses of pesticide or GM corn didn't consistently get sicker than those fed lower doses. In fact, some rats fed higher doses did better than the others.

Seralini offered no explanation why rats fed a pesticide should show the same pathology as rats fed genetically modified corn but not the pesticide, although Roundup and genetically modified corn are totally different things with, one would presume, different effects on the organism. That points to another shortcoming of the paper, which is that there's no explanation or even hypothesis of why either impurity should produce the tumors Seralini found.

"They don't show a plausible biochemical or molecular mechanism for the effect," observes Kevin Folta, a plant biologist at the University of Florida who has written critically about the Seralini paper. "It happens with two completely independent treatments, the herbicide and the [genetically modified] product, and to get the same unusual response from both is beyond suspicious."

The ultimate complicating factor is that the strain of lab rat Seralini used is predisposed to tumors, especially mammary tumors. By about 2 years of age, 80% of these rats will have them, on average. Therefore, the longer the experiment proceeds, the cloudier the data become, because most of the rats would eventually be tumor-ridden anyway. In other words, the length of the study isn't a virtue, as Seralini contends, but may be a flaw.

The dose-response and lack-of-mechanism stuff is bad, but not ultimately completely damning. Papers are published all the time that show some kind of association, but don't yet propose a causal mechanism in the body that explains the observation. Usually, what that means is that the scientific community accepts such a paper as an interesting observation worthy of further study, not as a dogmatic assertion of biological truth, and that's an important distinction against the reception of this paper: this is suddenly being treated by the anti-GMO crowd like absolute truth, even without those biological explanations, and that's bad.

And why isn't there a really viable biological explanation for Seralini's observations? Hello! Did you see that last paragraph? Allow me to repeat: "The ultimate complicating factor is that the strain of lab rat Seralini used is predisposed to tumors, especially mammary tumors. By about 2 years of age, 80% of these rats will have them, on average." Consider that with the fact that, as the article mentions, Seralini's control group was tiny, and you've got a pretty obvious foregone conclusion. Of course rats that grow tumors anyway will grow tumors when you feed them, well, anything.

Regarding Prop 37 itself, which Hiltzik argues against in his article: the scientist in me thinks it's really silly, because in my view the arguments against GMOs hedge into woo-based misinformation about how it has to be bad for you because it's not natural. It's that, or else people don't like Monsanto so they lash back at their GMO products. The pragmatist in me, though, thinks people can just have their labeled food. They can choose to eat what they want, even if it's based on exaggerated misinformation, because why not. In most other instances, I support people's decisions to control matters regarding their own bodies (being pro-vaccination is a notable exception.) I'm not entirely convinced, as the No on 37 lobbyists claim, that it will lead to increased food taxes/costs, but that's something I'll need to look into a little more. In short, I can't really endorse this proposition, because I feel it's based on quackery and fluff, but if labeled food increases the precious comfort and perceived bodily autonomy of the people of California, then all right hippies -- have at it.

"More trial, less error"

Here is an interesting article about reproducibility in science -- a really important concept that falls by the wayside more often than it should.

There is a daunting amount of research that is published monthly in every scientific field, including the social sciences. Papers often contradict each other, indicating unreliable results or results that are specific to the conditions in which the experiments were performed, or the group that was surveyed, etc. Many other published works, though, go unchallenged for months or years before anyone else attempts to recreate the experiment, or improves the experimental method or designs a new method. In this time, other work may be done that accepts these results as fact and begins a new phase of experimentation that builds on the inherent assumption that the prior work was true. This can result in impossible projects or increasingly stacked publication of unreliable data, if the initial assumption was a bad one.

This is why projects like the "Reproducibility Initiative," discussed in the linked article, are so important:

"‘Published' and ‘true' are not synonyms," said Brian Nosek, a psychology professor at the University of Virginia in Charlottesville and a member of the initiative's advisory board.
Last year, Bayer Healthcare reported that its scientists could not reproduce some 75 percent of published findings in cardiovascular disease, cancer and women's health.

In March, Lee Ellis of M.D. Anderson Cancer Center and C. Glenn Begley, the former head of global cancer research at Amgen, reported that when the company's scientists tried to replicate 53 prominent studies in basic cancer biology, hoping to build on them for drug discovery, they were able to confirm the results of only six.

The new initiative, said Begley, senior vice president of privately held biotechnology company TetraLogic, "recognizes that the problem of non-reproducibility exists and is taking the right steps to address it."

Those are some pretty awful statistics. Without knowing exactly what studies these scientists were able to reproduce, the use of the word "prominent" suggests to me that these could have been studies in higher-impact journals, which are supposed to have more rigorous peer-review and editing standards in order to avoid publishing sloppy science. The top journals are not completely immune to publication of "bad" or problematic studies, but it is supposed to happen less often.

The initiative is a great idea and offers an important service. We need more resources like this in science, double-checking results to verify their validity. We need these resources to be available in a trustworthy environment, so that lead scientists feel comfortable sharing their data and techniques without fear of getting "scooped" -- I believe that this (justifiable) fear is what prevents a lot of these checks from happening in the first place, so these "validation labs" would need to be neutral, non-competitive environments.

The diseases we are studying are complicated enough as is, and we don't need bad data or results obscuring their true nature and causes any more than the human body already does.

Sunscreen: Let Me Tell You About It

While reading this article today ("Sunscreen Myths And Misconceptions",) it occurred to me that writing my own post on the topic is long overdue. As a sunscreen disciple who has done a lot of research into ingredients and effectiveness, I've become very confident in my own sun protection, and dispense advise (both solicited and not) frequently to those around me.

I don't feel that I need to begin by justifying why sunscreen is good for you. Everything I've read that suggests otherwise is pseudoscientific bunk. Similarly, I don't want to spend a lot of time talking about cancer risk, since, again, the only people that deny that sunscreen decreases your risk of skin cancer are woo practitioners. I'd much rather delve into trying to break down some of the technical aspects of sunscreen itself and try to make it easier for neophytes and non-chemists to understand (yes there may have just been a GPB reference there.) If you're interested in the pesudoscience/cancer discussion, the link above does a good job debunking some of the myths behind anti-sunscreen proclamations.

First up, I want to talk about the difference between UVB and UVA, and what they mean for your skin.

source: http://www.skincancer.org/prevention/uva-and-uvb/understanding-uva-and-uvb

source: http://www.skincancer.org/prevention/uva-and-uvb/understanding-uva-and-uvb

In the most simplified terms, UVB gives you a visible, red, sunburn. UVB penetrates the outer-most epidermis only, and produce more severe immediate damage to those layers. UVA penetrates more deeply, and it will very rarely produce a red burn, but it primarily contributes to tanning and longer-term indicators of damage, like wrinkles and spots. Tans, though perceived as attractive, are actually evidence of sun damage, but since they aren't painful like sunburns, we tend not to think of them this way. (I should note that when I say "tans are sun damage" I am of course NOT referring to skin that is of a naturally darker complexion; I'm talking about the changing of one's complexion.) Both types of rays will contribute to skin cancer risk, especially over time; though, generally speaking, burns caused by UVB increase risk more immediately. This is a nice segue way to:

SPF and PPD
Probably everyone has heard of Sun Protection Factor (SPF); it's the nice number on your sunscreen that tells you how good the protection is. The SPF number informs you how strong the protection is with the following formula:

SPF X absorbs 1 - 1/X of UVB rays.
So for example, SPF of 30 absorbs (1-1/30), or about 96.7% of the sun's UVB rays. SPF 55 absorbs 98.2% of the sun's UVB rays. SPF 100 absorbs 99% of the sun's UVB rays. This is all why people say there isn't much of a point in spending more money on some of the higher SPF sunscreens beyond 45 or 50 -- because there isn't much of a difference between 98.2% and 99.0%, even though the 100 SPF is almost twice as high as SPF 55.

Astute readers who didn't fall asleep during the math section may notice that the SPF formula only covers UVB. That's correct! Persistent Pigment Darkening (PPD), the measure of UVA protection, has never been required information for United States sunscreens, so it's harder to judge how well a sunscreen will protect you against these longer waves. The best you can do is try to know your filters -- the exact chemical compounds in sunscreen that block or absorb UV radiation. This isn't always easy, because there are a lot of them, so I'll try to stick to the most important ones.

Physical Filters
The two main physical filters used in sunscreen are Zinc Oxide (ZnO) and Titanium Dioxide (TiO2). A "physical" filter means that the particles sit on top of your skin and act as a physical barrier to scatter, reflect, and absorb UV rays. Both of these two filters protect against UVB rays, but TiO2 has an absorption spectrum that only covers the shorter range of UVA: the "half" of the UVA spectrum that is closer to UVB, also known as UVA II. ZnO covers the full range of the UV spectrum, so sunscreens that use only physical filters offer much better protection if they include ZnO.

Chemical/Organic Filters
There are tons of these! So like I said, I'm going to try to keep it as simple as possible. Chemical/organic filters penetrate the epidermis and create an in-skin barrier that absorbs UV rays and metabolizes them into heat. It doesn't make you feel hot, not hotter than sitting in the sun anyway. It's just an energy-releasing reaction. And why the name "organic"? Well, organic compounds are literally those that have carbon in them, which these filters do, as opposed to the molecules that comprise physical filters. The two main things you need to be concerned about with when selecting sunscreens with organic filters are:
1. Coverage of the UV spectrum (like with physical filters,) and
2. Photostability.

The most common organic filters you'll see these days in United States sunscreens are Avobenzone, Octisalate, Octocrylene, Homosalate, Oxybenzone, and Octinoxate. Most sunscreens avoid using PABA these days, as it has been demonstrated to be potentially damaging -- so you should avoid sunscreens with PABA if you happen to see them. Avobenzone covers UVAII, and is the only one of these that protects against the longest-wave UVA rays up to 400nm, also known as UVA I. (Feel free to keep checking on the graphics above when I'm talking about short and long waves for reference!) The rest are all UVB filters, except for oxybenzone, which covers both UVB and UVA II. Oxybenzone is a good filter, but it does tend to be absorbed through the skin intact (rather than degraded into different, inert compounds) into the bloodstream more than the others. So far, no research indicates that there is any adverse effect from this, but if it makes you wary, you can avoid this filter. Due to the overlapping and complementary nature of these filters, they are often used together to boost UVB protection and cover the full UV spectrum.

So, what is photostability? Well, organic filters, as they absorb and metabolize UV light, are themselves degraded. Some degrade quickly enough in sunlight that they are considered photo-unstable. Avobenzone is one of these, but we like to see it in sunscreens because it protects against UVA I, while the other filters don't. Fortunately, sunscreen makers have found a way to stabilize it in solution by adding octocrylene. So that's a good green flag: if you see avobenzone and octocrylene in a sunscreen, chances are it's in effort to stabilize avobenzone so that it lasts longer. Avobenzone also has an enemy, though: it's already unstable on its own, but if you add octinoxate to the mix, it helps degrade avobenzone even faster! If you need help remembering this, a mnemonic that has helped me remember is "OctiNOxate," as in "octiNOxate is NO GOOD with avobenzone."

Why is photostability important? Well, first know that it is better to wear an unstable sunscreen than no sunscreen at all, since you're at least getting some protection. Beyond that, a photostable sunscreen is important because most people don't reapply sunscreen throughout the day when they are in the sun, and a stable sunscreen will simply last longer and offer better protection for longer. If you are the type that doesn't mind conscientiously re-applying every 2 hours, then maybe stability isn't as much of a concern for you. But I'd say that type of person is about 5% or less in the population, so most of us are better off seeking out photostable sunscreens.

I also want to talk about two other filters that have been prevalent in European sunscreens for at least 10 years, but are either not approved or very recently recently approved by the FDA here in the US. Tinosorb S and Mexoryl are both broad-spectrum filters that absorb the majority of the UVB and UVA spectrum, with drop-offs in absorption toward the extreme ends of the spectrum (as with all filters.) They are also both photostable, and Tinosorb actually can also stabilize avobenzone in solution. These are awesome, multipurpose beasts of UV filters, and the FDA is just taking forever to approve them. Come on, FDA! Fortunately, sunscreens using these filters are not too difficult to get online.

That should about wrap it up. In summary, here is what you should consider when selecting a sunscreen:

1. Physical or organic filters? Generally, the recommendation seems to be to start with organic filters and see how your skin takes to them. If you have sensitive skin or find that you react to most sunscreens that use organic filters, it may be time to get physical. If you're doing so, make sure you get one with zinc oxide, since that provides the best protection.
2. If organic works for you, make sure it has stable, broad-spectrum filters. Look for 30+ SPF sunscreens with avobenzone and octocrylene, first and foremost -- not one or the other. If they also have homosaliate and octisalate, that's fine; they're just contributing further UVB protection. Same goes for oxybenzone, unless you'd rather avoid it. If you can find sunscreens with Mexoryl and Tinosorb, try those out too! (They're personally my favorites, but that's not a scientific bias so much as what formulations I like best from experience.)

I hope this all helped! If there is interest, I can do a separate post for questions and/or my personal sunscreen picks!

Vaccines are a good thing.

News of the recent whooping cough epidemic in Canada has me putting on my raging boots for another science rant. Anti-vaccination rhetoric is an unfortunate consequence of insufficient science literacy and, in some cases, religious dogma. It is difficult to touch the religious crowd with respect to their beliefs, but there are plenty of others out there who are anti-vax simply due to ignorance and misinformation.

Most of the furor over the possible autism-vaccines connection stems from a 1998 paper published by Andrew Wakefield et. al. in the medical journal The Lancet. The paper suggested at a causal link between the MMR vaccine and ''regressive autism" -- autism that develops over time in children that were seemingly neurotypical before -- in 12 young patients. The paper has been thoroughly debunked, and was completely retracted by Lancet in 2010. Wakefield himself has been found guilty by the British General Medical Council of "serious professional misconduct" and struck off the medical register, effectively banning him from ever practicing medicine in the UK again.

As scientists, we don't just stop there. We conduct independent investigations. And what have we found? The Institute of Medicine, over the years, has conducted several in depth reviews of the medical and scientific literature as it relates to all varieties of vaccines and adverse health outcomes. Though in rare cases, their studies have found side-effects of some vaccines in individuals, again, there is no suggestive link between vaccines and autism."But there are side effects!" Well, yes. Of course there are. Just like how some people are allergic to shellfish, and some people experience side effects from, well, any other medication on the market, and any other substance on the planet, some people have reacted poorly to vaccines.

It is truly disappointing to me that concepts of statistical risk and social responsibility, ideas that most people generally seem to understand, suddenly seem to vanish when the subject is vaccination. Some people actually don't know about herd immunity (though everybody should,) but even some who do know still cross their arms, cover their eyes, and insist that they have the "right" to decide what is best for their child. And of course, they do. But when all evidence points to vaccination being what is best, this line of logic indicates nothing other than ignorance, and even hubris, on the part of these parents.

So, what can the rest of us do to combat conspiracy theorists, protect ourselves and others, and raise awareness?

1. Get vaccinated, obviously, and make sure your family is vaccinated too. As adults, do you know that some of your vaccinations lose their effectiveness over time? Have a blood draw and request a titer test be done to check for your immune status against diseases covered by the regular vaccine schedule. Consider the Tdap booster as an adult, which covers tetanus, diptheria, and pertussis (whooping cough.)
2. Educate yourself about estimated herd immunity thresholds in your community, and talk about vaccinations in your social circle. Are your friends vaccinated? Are their friends vaccinated? Are their friends' and families' children vaccinated?
3. And as long as you are going to be talking with other people, be armed with factual, science-based information about the safety and efficacy of vaccines both at the individual level, and at the community level. The links I provided above are a good start, but feel free to dive into primary sources if you are comfortable with scientific jargon. Avoid as sources websites that have an obvious agenda, and that present "evidence" in the form of links to other websites with a similar agenda. You can follow these arguments around in circles and find a lot of charismatic people saying persuasive things, but if they don't back their words up with peer-reviewed, medical evidence, be wary.
4. If you care for anyone who is particularly at-risk for any of the vaccine-controlled diseases, make sure your home is a safe space for them by only having vaccinated guests. This is awkward and tricky, but it protects the health of your loved ones. And if enough people do this in practice, it can have the effect of exerting social pressure on those who aren't vaccinated for dubious reasons.

These things may be small, but misinformation often spreads between friends and acquaintances in meatspace (offline.) Parents are fanatical about their children, and sometimes a persuasive bad idea, left unchecked, can transform otherwise rational people. Make sure that doesn't happen to the people you know!

Equivocation and inconclusive science

I was disappointed to read a recent post from a feminist/skeptic blogger who I usually like. Stephanie Svan's post, Broken Chromosomes and Damaged Brains, refers to comments made on a panel that discussed gender differences (broadly.) Here is the question that prompted the post:

The first statement, called sexist by many viewers, was Heina Dadabhoy’s comment that the Y chromosome is a broken X chromosome. The other, called outrageously sexist, was Greg Laden’s statement that the male brain is a female brain that has been damaged at various times throughout development by testosterone. The question is, however, are these statements true?

Fair enough premise. The post first investigates the claim regarding the Y chromosome, using this article from the Howard Hughes Medical Institute as its reference. The evolution of the Y chromosome essentially stems from a series of self-inversions that left it structurally different from the X; these drastic differences left the X and the Y unable to recombine. Without these recombinations, the Y then was subject to a series of deletions that left it smaller in size. Given this evidence, the post claims that indeed, it is not factually incorrect to say that Y is a "broken" X:

This [evolution] has undesirable consequences for male humans[...], at every stage of development. A short sex chromosome means that males have only one copy of some genes. Sex-linked hemophilia is one of the specific vulnerabilities of males caused by this arrangement. There are plenty of others, and there are a number of vulnerabilities that we’re still not sure to what degree are sex-linked and to what degree our screening processes and social expectations make it more likely that males will be diagnosed. Some of those may also turn out to be attributable to having a Y chromosome.

So, yes, the X chromosome is the original in this situation, and the development of the Y chromosome both depleted the X chromosome and did so in ways that are not helpful to those who carry it. It is a broken X chromosome.

In my view, there are some problems with this argument. Simply evolutionarily speaking, the Y chromosome has stabilized and has only lost 1 ancestral gene over the last 25 million years. Additionally, the Y chromosome contains close to 100 unique, functional genes, and it shares more functional genes with the X.

Scientifically, then, I don't think it's as factually accurate to say that Y is "broken" as it is to say that Y is simply "changed" or "altered."

With regard to the comment about "damaged" male brains, the post says:

...it is very difficult for us to tease out what causes the differences observed between male and female brains. There does seem to be a role for testosterone (used generically for androgenizing hormones) during gestation in the establishment of gender identity...

The best information we have suggests that any differences between the function of male and female brains tends to be quite small and unimportant relative to the vast similarities in the capabilities that we find when we compare the two. It is decidedly not enough to account for the large differences we still see in opportunities and performance between men and women.

Essentially, the role of testosterone in brain development is pretty murky. We're not really sure what the role of testosterone is, period, so using loaded terms like "damage" is an inflammatory supposition. The post defends the term, though, with the following:

There may, in fact, be some skills that men are better at than women by virtue of masculinization of a female brain due to the presence of higher levels of testosterone in males.

However–and this is a very important however–Greg’s statement about testosterone damaging female brains to make them male is true to exactly that same degree...

If you have a complex system that is capable in a general sense, and you retool it to specialize, you lose some of that general capability. In other words, you have damaged the ability of that system to generalize.

To make this more specific to hypothesized sex-related differences, if you take a cooperative system and retool it to be more competitive, you have damaged its ability to cooperate. If you take a highly verbal system and retool it to a more spatial system, you have damaged its verbal abilities. If you take a “female brain” (whatever precisely that is) and, through the application of testosterone, retool it to act like a “male brain” (whatever precisely that is), you have damaged its abilities as a “female brain”. How can you have done anything else?

Svan is saying, more or less, that a testosterone-induced male brain is not damaged in general, per se, but it is a damaged female brain; it's damaged in its ability to be whatever female brains are. She is making this semantic distinction, and arguing in favor it it, because of the implicit, unchallenged assumption that men are people, and women are a different, specialized kind of people (for a fun post that illustrates this idea using bathroom signs, check out this post about how men are depicted as people, and women are people in skirts.) Referring to biological standards of maleness as 'damaged' and 'broken,' she theorizes, satirizes the common rhetoric that maleness and masculinity are improvements.

Now, I'm going to editorialize. For starters, though I'm critical of this post, I'd like to state that I infinitesimally small levels of sympathy for men who loudly shout down women who experience tangible, real-life, day to day sexism (for instance, sexual harassment) but scream "MISANDRY!" over an abstract comment about the Y chromosome. Obviously, I have no issues with people who look critically at sexism against men and women, because that's what we all should do.

Primarily, I'm critical of the choice of language because I really don't think there is the scientific merit to back the language up, just like I don't think there is scientific merit to demonstrate male brain superiority at math, for example. As one commenter said, "When certain forms of feminism is (sic) shown to be without scientific merit, we should abandon them for more evidence-based forms of feminism, not zealously defend them as obviously true by substandard arguments." Svan has sidestepped this criticism in the comments by suggesting (my interpretation, not her words) that the post isn't really about the science, but about the satire. The science, here, merely establishes that the accused statements are not factually incorrect. The intent of the language is more important.

I understand her point, but I think it's gotten too esoteric for its own good. She's doubling down on words that may not have been carefully chosen (or they may have been, but by Svan's own admission, in the context of a panel discussion, elaboration on the intent of the language wasn't possible) and creating an advanced-level discussion out of some pretty casual statements. As another commenter said, "The fact that two throwaway sentences had to have pages of text written to justify them, seems to be an admission that most aren’t going to get it on first blush. What of the people who hear that line, but don’t get the benefit of this massive footnote explaining the language choice?"

Because I like her general idea of satirizing the concept of male superiority, I might have constructed the whole argument focusing just on the semantic aspect. Personally, though, I wouldn't try to justify the statements, because as social justice types always say, "Intent isn't magic." I would, using the responses as evidence, make the point that "Isn't it interesting, that when maleness is presented as a lesser form of femaleness, men don't like that very much? Could they maybe see how, when the reverse occurs, as it often does, women don't like that very much?" I wouldn't care so much about trying to demonstrate through the scientific aspect that "it's kind of true!" I'd want to focus on how these men seem to be very perceptive of pervasive sexism when it's directed at them, but have no problem silencing women when they speak out about the same. I'm not interested in defending problematic language; I'm interested in getting people to explore their empathy by recognizing problematic language even when it doesn't apply to them.

"...genetic determinism of disease is a reductionistic fallacy that is now collapsing."

I received an interesting email today as part of a loose group of geneticists, statisticians, epidemiologists, and molecular biologists that my mentor participates in regularly. It was a forwarded rant, pasted in its entirety below, from Jonathan Latham, Executive Director at the Bioscience Resource Project.

Dear Friends and Colleagues

In the eighteen months since we published (to some scepticism) The Great DNA Data Deficit: Are Genes for Disease a Mirage? there have been important developments in human genetics that are relevant to the food and environmental movements worldwide, and that deserve to be very widely known.

In particular, two scientific publications, the first from Jan 2012:

The mystery of missing heritability: Genetic interactions create phantom heritability by O. Zuk, E. Hechter, S. Sunyaev and E. Lander in the Proceedings of the US National Academy of Sciences.

This can be found at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268279/

and even more recently, from April 2012:

The Predictive Capacity of Personal Genome Sequencing by NJ Roberts, JT Vogelstein, G. Parmigiani, KW Kinzler, B. Vogelstein and VE Velculescu in Science Translational Medicine.

This can be found at: http://www.biostat.wisc.edu/~kbroman/hgjc/hgjc_2012-04-13.pdf

These papers have powerfully vindicated the scientific conclusions of our article. We draw your attention to three noteworthy aspects:

1) the lead authors of each (B. Vogelstein and E. Lander) are among the most highly cited biomedical researchers in the world

2) that their analyses, though new, are based on data that has been available since the human genome was sequenced. It is a rethink, not new data.

3) these papers demonstrate that leading medical geneticists no longer have realistic expectations that most human disease occurrence can be explained by inherited genetic predispositions.

In other words, genetic determinism of disease is a reductionistic fallacy that is now collapsing. Geneticists now face a long retreat from Moscow and the interesting question of who will rewrite the textbooks and tell the public.

We would also like to point out some others who have stuck their necks far out and predicted these events long before we did.

Joseph D Terwilliger and Kenneth M Weiss Linkage disequilibrium mapping of complex disease: fantasy or reality? Current Opinion in Biotechnology 9: 578-594 (1998)

Jay Joseph (The Gene Illusion, 2004) http://jayjoseph.net/the_gene_illusion

Helen M. Wallace (2006) A model for gene-gene and gene-environment interactions and its implications for targeting environmental interventions by genotype. Theoretical Biology and Medical Modelling 3: 35-58.

One last point is perhaps worth making. It is important to appreciate that, with a few exceptions, research geneticists have not merely been wrong in this matter, but that they have actively and grossly misled society as a whole. They could have and should have known that genetic predispositions might after all explain very little in the way of disease, but they routinely failed to make clear that possibility and went far beyond the actual evidence in order to obtain public funds and prestige. Caveat emptor.

yours sincerely

Jonathan Latham and Allison Wilson

What I find interesting, both in this casual email and in some of the linked articles, is the accusation of deception. I'll grant that in a research landscape that promotes harsh competition and limited rewards only for those at the very top, the "significance" section of many grant proposals may be often overblown in order to try to secure funds. However, this exaggeration is done with the completely transparent knowledge that the reviewing committee is not stupid. We are scientists communicating with our peers (other scientists) and it is not likely that this exaggeration is fooling anyone. 

There is also the fact that many geneticists, rife with excitement, have communicated regularly with popsci and lay press regarding the possibilities that lie ahead in genetics. Here, though, is where I raise the question of intent. Latham's email says "research geneticists have not merely been wrong in this matter, but that they have actively and grossly misled society as a whole." I find this statement to be grossly misleading, itself. When the Human Genome Project was completed, yes, you couldn't take ten steps in any direction without tripping over an article about how genetics was going to solve all of our medical problems. But in more recent years, I've been hard-pressed to find statements by respected geneticists that still make such claims. Heck, I even wrote about this myself over two years ago (cliff's notes: we don't have enough knowledge or genetic information to actually give someone a definite measure of their likelihood for developing diseases.) What you're more likely to find, in my opinion, are statements like mine from geneticists that are optimistic but that are representative of the theme that there is still so much we don't know, and THAT'S why continued research is important. It's absolutely not because we think we are trying to convince anyone that we already have the answer, and just want more money ... just because.

The linked January 2012 paper from Zuk and Hechter presents the idea, as if it's a novel one, that interactions and pathways between genes, as well as interactions between genes and the environment, are more likely to explain complex disease pathology than genetic heritability alone. Allow me to remove my 'serious hat' for a second when I say: Well, duh! Labs have been exploring GxG (gene-gene) and GxE (gene-environment) interactions for years, but the problem? It's hard. At present, the mathematical and statistical models available to us cannot adequately address these interactions, but tons of labs are working on it. 

I have long been frustrated by the way that science research as a whole is portrayed and reported on in the popular media. I think that these misrepresentations of more responsible research are at fault for any misconceptions that society at large has regarding genetic research or biomedical science in general. I do not believe that the blame lies at the feet of geneticists, who are constantly adapting their work and techniques to incorporate and address the newest ideas and knowledge in the field.


Now, my whole response here is an OPINION piece, so, as with anything op-ed, citations needed.

Book review: Oryx and Crake by Margaret Atwood

I’m not really going to be fair to this novel — just throwing that out there. Oryx and Crake is a dystopian novel with genetic engineering/biotechnology as its cause célèbre. In the present, all “organic” humans are dead, leaving only behind the protagonist, Snowman, and a small race of humans that Snowman refers to as “Crakers.” How Snowman came to be the only living human from prior generations is initially a mystery, but it is unfolded throughout the novel in flashback format.

There is a lot in the plot to unpack, and I won’t go into it in detail. This book is much more interesting for its thematic elements. In addition to tackling the ethnics of biotechnology, Oryx and Crake also discusses commercialism and consumerism, class segregation and education, and sexuality and objectification. These themes are really the meat of the novel; everything that occurs in Snowman’s flashbacks serve as opportunities for him to critically ponder the implications of the situation. It’s not really a morality play, though, because a lot of Snowman’s choices are made for him. He is just dealing with the repercussions, and has the benefit of perfect hindsight as he’s looking back on his life.

So why did I earlier say I’m not going to be fair to this novel? Well… it’s hard to explain. Novels like 1984 and Brave New World have a lot to do with psychological conditioning, and the ‘nurture’ side of things. For whatever reason, I never had difficulty accepting that this kind of manipulation could happen in real life, and that’s what made those particular stories so compelling for me (and others, I suspect.) On the other hand, novels like Oryx and Crake tackle ‘nature.’ It’s about tangible, scientific manipulation that causes animals and humans to be different from what they once were. Of course, there are real life foundations for this — GMO food is certainly controversial enough, and we use genetically-modified animal models regularly to study gene function and disease pathology. We’ve floated theories that we would eventually see ‘designer babies,’ where parents could select for certain genetic variants that improved their children’s overall fitness (in the Darwinian sense.)

I don’t know, maybe my imagination is finite and it just ends before this novel begins. But I just don’t see it coming to this. There are only a few elements in here that seem scientifically feasible, and I’m not just talking about now — I’m talking about not being feasible ever. And unfortunately, not being able to suspend my disbelief did detract from my overall satisfaction with the story. I’m not saying that it’s not good, or that it’s not well-written, or that there aren’t some really gut-wrenching moments. Overall, it’s actually pretty compelling; it’s one of those books that stays with you for awhile. So despite my personal limitations, I do recommend this one for fans of dystopic books.

Book review: The Dispossessed by Ursula K. Le Guin

 X-posted at Cannonball Read IV

Here we have the story of two worlds: Urras and Anarres. Urras is meant to be an analog of our Earth, and Anarres is described as its habitable moon, albeit harboring some pretty tough conditions. The main plotline is constructed in parallel around the protagonist Shevek, a theoretical physicist, mathematician, and Anarresti. He grows to feel the necessity of traveling to Urras in order to progress further in his field, an action that is welcomed by Urras and abhorred by his fellow Anarresti.

Anarres was founded as a refuge for a colony of what may best be described as uber-communists or collectivists, based on our language. The title “The Dispossessed” refers to their extreme disavowing of anything insinuating personal possession: a blanket that I usually sleep with is not “my blanket” but “the blanket,” and an offer to share the blanket is not “Would you like to share my blanket?” but “Would you like to use the blanket that I use?” They are anarchistic and accept no government or currency, and they volunteer to perform work where it is needed, sometimes based on special interest or talent, and sometimes not. Shevek describes Anarres (I am paraphrasing here) as a place where it is not easy to live, but it is rewarding.

And if Anarres is the most extreme form of communism, then on Urras we are treated to the most extreme form of capitalism. As a capitalistic society that tends to pontificate often about our bitter end, we have a better idea about what that may look like: class warfare, feuding nations, and some totalitarianism thrown in for good measure.

For obvious reasons, the two societies don’t understand each other, but the Urrasti are portrayed as having more of a curiosity about Anarres, while Anarresti find even the neutral mention of Urras to be distasteful and can’t fathom the appeal whatsoever of such a place.

The Dispossessed explores politics, economics, religion, and of course  — it is Le Guin! — gender issues. It’s beautifully constructed around all of the aforementioned social issues, but also around Time, the focus of Shevek’s study. Shevek spends the majority of the novel developing his “Simultaneity Principle,” which is essentially a new way of explaining Time that incorporates physics, philosophy, and mathematics, and does not subscribe to the linear model of time we are familiar with. As such, the novel doesn’t progress in a strictly linear fashion. The chapters alternate between taking place on Urras and Anarres, with what are undoubtedly different periods of time in Shevek’s life unfolding simultaneously. Le Guin is a master at these “fish out of water” stories that result from the meeting of people from such starkly different backgrounds. It’s a pretty dense read and something that will take several sittings to get through, but regardless I wholeheartedly recommend it. The Dispossessed, for me, is poignant, provocative, and above all engaging.

This is why America's science education needs to step up its game... NOW

pegd said... I have 4 boys. When I was pregnant with #4 the odds were less than 20% for it to be a boy.

Char said... the chances of having a girl is around 50%. For each pregnancy. No matter how many boys you've had before. (ding ding ding!)

fairylights said... 50% per pregnancy, although there are some, er, natural ways to try and swing the balance in your favor. One of them worked with our third child, but they sure as heck aren't full proof. (?)

Mooshki said... Actually, pegd, if all of your kids have the same father, I think the odds were even better than 50/50 that your fourth would be a boy, because the first three were a sign that he has a genetic predisposition to father sons. (facepalm)

pegd said... Yes Mooshki, you're right, my ob/gyn told me I had less than 20% chance for a girl with the last one (think the actual # was around 15%. My boys have the same father. (Your OB/GYN needs to go back to medical school... or take high school statistics, post haste.)

Why I won't be paying to see The Social Network - Part 2: Hapless Geeks

continued from part I here

Despite the seemingly never-ending barrage of celebrities, Hollywood types, and generally pretty people who insist that they were heinous looking geeks in middle and high school, I'm personally fairly certain that they all doth protest too much.

Reason being, I kinda have to think that if these people were all geeks and nerds, then they'd actually manage a somewhat realistic portrayal of geeks and nerds in the media.

When responding to the criticism of The Social Network that it was a bit unseemly with its management of women, Aaron Sorkin said "I was writing about a very angry and deeply misogynistic group of people. These aren't the cuddly nerds we made movies about in the 80's. They're very angry that the cheerleader still wants to go out with the quarterback instead of the men (boys) who are running the universe right now." Two things:

1) Let's be real - the "cuddly nerds" of 80's movies thought about as highly of women as the misogynistic geeks of The Social Network do. It was just played for laughs. I'm using Revenge of the Nerds as my frame of reference here, but I'm sure there are more examples. For one thing, there are at least two scenes in the movie that are not only deeply disrespectful of women; they're also illegal. One is the bit where a video camera is installed in the sorority house so the nerds can watch the girls walk around topless. The second is the part where the nerd ends up having sex with the popular hot cheerleader even though she thinks it's her boyfriend. Let's be clear about this - in a court of law, that would be called rape. In the movie, she's all "Oh nerd I can't believe you were so good at t3h sex!" Yes, that's a very realistic response from a woman who just found out she had sex with some random person pretending to be her boyfriend in the dark.

2) Yes, there is misogyny in the geek world. There's misogyny in every world. This is nothing new. What's interesting is the depiction of this geek world as such a frightfully misogynistic one.

In the STEM (science, technology, engineering, math) fields women are still a minority, except for probably the life sciences (heyo!) We know this. And yes, some geeks are mistrustful and resentful of women, dating back to whatever experience that has left them scarred. But geek men are now being raised in the post/feminist era, and increasingly with post/feminist ideals. Many geeks now are mildly awkward, but still have daily successful (even pleasant!) interactions with the opposite sex. And with so much of STEM work now being highly collaborative, chances are that there are male and female geeks working well together on a variety of projects.

This is why The Social Network rings false. Facebook is exactly the type of project that is born out of a team of collaborators that probably includes women (which real life corroborates,) but the movie instead opted for a radical portrayal of Facebook's creator as, frankly, misanthropic in general, but particularly seething toward women, to the extent that he apparently didn't want any on his team. (Well, I think one woman was spotted among the coders, but there was some kind of sexual remark made about her as well.)

So while geek women have stories to tell about sexism in the workplace - and they do - observing the geeks in this movie purports to be a surreal experience because it is so jarring against what a lot of geeks actually experience in real life. Even though Revenge of the Nerds and The Social Network are, at the end of the day, both stories about how geeks end up running shit, both treat geeks like they are a specimen to be studied. Like women, Hollywood just doesn't seem quite comfortable portraying the geek experience - male or female - because it hasn't quite lived it (as much as its members claim to have done so.)

Geeks - we walk among you. We look like you and talk like you, and we're not overall a collective group of social degenerates that do horrible things in movies out of despair against humanity. We do get laid and usually, it's by a real, live person. I know it seems like it's asking a lot for the contents of a fiction movie to be realistic, but hell, for a movie that's getting so widely praised (again, probably by people who are more than happy to make geek culture a scapegoat for sexism, human nastiness, and antisocial tendencies in general) I'd like to see characters that have some basis in real people - and not in name alone!

Day 09 - A photo I took

This is probably the most awesome photo I've ever taken. It happened by sticking my camera lens just so into the eyepiece of a telescope.



Goodnight, moon...

Day 06 - Whatever tickles your fancy

Well, why not use this time for a general life update?

Since I last wrote, I finished my first year of grad school and started apartment hunting for a spot to live closer to campus, but not necessarily in one of the seedy surrounding neighborhoods USC is known for. Though we're currently shopping around in South Pasadena and the Los Feliz/Silverlake area, our limited budget so far seems to be yielding only some of the crappier apartments available to us. But we're hoping that someone will post a listing for a little gem one of these days and we'll snatch it up! What a fantasy, eh?



On the school front, it's been an interesting year. I've oscillated between varying poles of confidence - on the one hand, my moderate apathy about my coursework sets me apart from several of my classmates, who noticeably take more time to study and therefore tend to actually get that A. I, on the other hand, am content to just keep the 3.0 that's required of me and care more about the lab, but it still makes me feel like a slacker at times to just be shooting for the average.

On top of that, I'm finding that when I leave campus, I'm just not interested in talking about science. Does that make me a Bad Scientist? Does it disqualify me from being Someone Who Knows What They Are Talking About? I dunno - I'm just around it all day, and when I leave, I want to talk about something else. So again, I feel a little unworthy when I go out with some of my friends from the program and they're all talking about their lab stuff, and they ask me how it's going, and I'm just like "It's great."

That said, I got a huge confidence booster two weeks ago when my application was accepted to be a CIRM Fellow. (CIRM is the California Institute for Regenerative Medicine, aka our state stem-cell initiative.) I didn't know how competitive of an applicant I was as a first-year grad student without any papers, but I knew that my research background was strong, and that the proposed project itself was awesome. But, I did it! This is such a huge relief to me and the lab - all of the funding (by which I mean, funding for the research materials and funding of my salary) are now covered by CIRM for one year - and potentially two based on progress of the project - and my PI mentor doesn't have to worry about scraping money together to pay me. So yeah, this is really kind of a big deal. And, by extension, since I'm using this as a motivator to actually believe in myself, I'm kind of a big deal. And I deserve to be here.

And that about sums that up!

Ideally this will be cute enough to carry me through the rest of a boring day of studying

"I’m detecting microscopic amounts of cuteness"

ENHANCE!!!

Tori S. says: “One of the biology professors at my college breeds angora rabbits. She brings them in for the students to help socialize, so they’ll be nicer pets (don’t worry, they’re not for experiments!!!) It couldn’t be better timing than right now, what with finals coming up and everything. So, a bunch of us took picture of/with the bunnies.”

(thx Cute Overload)

News-ish stuff from this week...

Consumers Slow to Embrace the Age of Genomics

I've got a bit of a problem with this article, particularly the headline. I actually read a Cracked article earlier this week that discusses the exact phenomenon the NYTimes article engages in (scroll down to #4 on Cracked to see what I'm talking about.) That is, the headline makes it sound as if the focus of the article is that there is this great new Age of Genomics dawning, ripe with possibility (somewhat true) but that the bumbling consumers are too "slow" (see what they did there?) to accept it.

Page 1 - the "money" page, the page they expect most will actually read - extolls the woes of companies that offer to sequence DNA samples from customers and give assessments of individuals' increased or decreased risk for certain diseases based on their DNA. Their problem? No one's buying. The article offers the possibility that it's too expensive, and then finally this gem is revealed:

But the services face an even more fundamental problem: in most cases, the current level of DNA scanning technology and science is unable to offer meaningful predictions about the risk that a person will get a disease...

... what has become clear to geneticists only in the last year is that the genetic variations known so far can explain only a very small part of the risk of getting most diseases. The rest involves still unknown genetic factors or environmental ones, like a person’s diet. Experts say that, for now at least, in most cases there is little a person can do to act on the information from genome scans.

That quoted bit? That's the truth. That's the long and the short of it. There is no reason at this juncture for someone to spend the money these companies are asking for a full genome scan because we don't have enough information to actually give someone a definite measure of their likelihood for developing diseases with genetic and environmental components.

What's funny is that on Page 2, the article actually continues to reveal more truthiness, such as that identical samples sent to different sequencing companies came back with conflicting results. So by the end of the article, anyone who actually took the time to read it would probably understand why these companies are struggling: it costs too much for little to no benefit. So what's the deal with that headline blaming the public for not embracing our future? It kills me.

Hey Men – Don’t You Dare Blame Sandra for Jesse James Cheating!

There's not much I really need to say about this. Basically, the author recalls talking to male friends about the scandal that broke this week, and the guys blamed Sandra Bullock for leaving him alone with his penis too long. Are these bitches for real? The article itself isn't a super strong rebuttal, but one of the commenters did a pretty good job of summing up what's wrong with that logic:

Lisa McLeod: Men who use a wife’s absence to justify cheating belong in the same category as people who sue McDonald’s for getting them fat.

Question for those men – What would you say if Barbara Bush, Hillary Clinton or Michelle Obama hooked up with the white House kitchen help because hubby was distracted by his job and – whine whine- just wasn’t paying enough attention to his wife?

In other words? Suck it up! If you get married, you're making a commitment to someone who you supposedly love; in addition to that, you're making a commitment to be monogamous. If either of those commitments is something you think you can't keep, don't get married. End of story!