End of semester madness!

What am I up to? I’m writing a “fake” research proposal for one of my classes on doing a genome wide association study and exome sequencing to search for genetic components of homosexuality. I say “fake” because it’s a project for a class, not something I’m actually submitting to the NIH or NSF. Well, I mean, I could theoretically submit it as a grant if it ends up being super awesome and a mind-blowing scientific idea, but at this rate I’m just trying to not embarrass myself when turning it in.

On top of that I’m attempting to finish my actual research from this quarter since our presentations are next week. I’m not nervous about the speaking part – heck, I do that for fun now – but talking about science is a bit harder than making jokes about atheism. So, yeah, again – aiming for not embarrassing myself. Frantically trying to learn R to make my graphics, since my professor nearly had an aneurysm when he saw I was using Excel to make my charts.

Aren’t the end of quarters great?!

I know a lot of you are also students – consider this an open thread to complain about all the work you have to do and to procrastinate doing it. Non-students welcome to whine too.

And the media sensationalizes science again

I came home to a flurry of emails, tweets, and blog posts about NASA’s big announcement. I was momentarily floored when I saw headlines like this:

“NASA Finds New Life” – Gizmodo

“NASA-Funded Research Discovers Life Built With Toxic Chemical” – The Richard Dawkins Foundation

“Bacteria first species observed to use arsenic-laced DNA backbone” – Ars Technica

Though upon actually reading about the discovery, the most accurate title came from Boing Boing: Weird life form on Earth – kind of, maybe.

Look, it’s an exciting discovery, but everyone is over-hyping it. This bacteria is not an arsenic-based life form in the sense that we are carbon-based life forms. It does not use arsenic as a source of fuel. It does not exclusively build its DNA backbone using arsenic. It doesn’t even really like to do that at all in the wild – it incorporates arsenic under laboratory conditions that force even higher concentrations of arsenic upon it. It is not a different type of life that arose separately from phosphate-using lifeforms.

What it is is an excellent example of evolution. While coming from a phosphate-using ancestor, this bacteria has somehow adapted to an extreme environment that would kill most other organisms. I’m more interested in how it avoids death by this toxin than the fact that it incorporates a molecule extremely similar to phosphate into its DNA. PZ has a more thorough scientific breakdown over at Pharyngula.

Way to go, shoddy science reporting. Creationists are probably wetting themselves over this “new life form,” ready to tell biologists how it could have only been designed. I mean, just look at how this redditor is reacting to your sensationalism:

Is it ok that I’m already discriminating against arsenic based life forms because they are fundamentally different than me? Bunch of arses, they are.

Sigh. Well, at least I don’t have a whole new DNA structure to memorize. Getting a PhD in Genomics was already hard enough.

Philosoraptor, the geneticist

Discussed in one of my classes yesterday:
The corollary was “If a gene falls in the woods, does it make a noise?” This is what happens when you give grad students too much coffee.

Genetics geeks – feel free to discuss.

Why my building has key cards


Now I just need to figure out how to make the doors say “Good morning, Ms. McCreight” instead of “Beep.” Then I’ll really be living in a sci-fi movie.

(Alternate reason why my building has key cards: To keep the undergrads out. I like my reason better.)

EDIT: I originally had pi = 0.6 because my project is currently looking at heterozygosity in humans, which is represented by pi, but I realized the inevitable nerd rage I would invoke when people would think I was too stupid to realize pi (approximately) = 3.14. So x it is.

…I have become too nerdy to make nerdy jokes, gah.

Compared to the rest of the tree of life, your sex life is boring

Man, the news seems to be Animals After Dark the last couple of days. As a sex-obsessed biologist, I can’t exactly complain. Here are some neat stories:

  • Male wasp spiders only get one chance at love, since females eat them after mating. How romantic. It used to be believed that males preferred larger, more fertile females, but it looks like what male spiders really dig are virgins. I guess it’s not a bad strategy when the first male to mate with a female is most successful. Well, as long as he remembers to snap off his genital inside of her to form a chastity belt. (What, did I make some of you uncomfortable? Look, I had to stare at a scary spider to read that article for you, so shush)
  • Move over, Mary. A female boa constrictor has given virgin birth twenty two baby snakes. Parthenogenesis – the development of an embryo without fertilization from a male – has been documented in reptiles before, but this case is unique. You’re probably familiar with how sex is determined in mammals – XX are female, XY are male. It many reptiles and birds, the homogametic (same sex chromosome) sex is reversed – ZZ are male, ZW are female. The surprising thing is that all of the virgin offspring were WW, which was previously thought to be nonviable. They are all essentially half clones of their mother, resulting in a duplication of just half of her genome. That, or God is sending an interesting message with his species choice for the second coming.

Natural genes no longer able to be patented

From the NY Times:

Reversing a longstanding policy, the federal government said on Friday that human and other genes should not be eligible for patents because they are part of nature. The new position could have a huge impact on medicine and on the biotechnology industry.

I feel as someone starting their PhD in Genome Sciences, I should have a nice elaborate analysis for you… but alas, I don’t. I can tell you all about how genes work, or how to isolate them in the first place, but I’m no expert on the pros and cons of gene patents.

I have my ideas, but feel free to discuss in the comments. Do you think this is good or bad for future research? For future medicine?

No genetic testing project for UC Berkeley freshmen

The University of California Berkeley was planning an innovative and somewhat controversial “common freshman experience” for its incoming class. Rather than forcing everyone to read some book no one really likes written by their professor (*cough*Purdue*cough*), they decided to let freshmen voluntarily be tested for various benign yet interesting genetic traits. It’s purpose was to start dialogue on the future of genetic testing and personalized genomics.

However, the California Department of Public Health has recently decided that students are not to receive their personalized results, and only aggregate data can be presented:

“They said that we were providing students with information that could affect the treatment of disease or the evaluation of health,” said Mark Schlissel, dean of biological sciences in Berkeley’s College of Letters and Science. “We disagree with the California Department of Public Health.”

According to the department, laboratories conducting clinical testing — which can diagnose a disease or monitor treatment — must be licensed and have certification for reliability and accuracy. Excluded are labs running samples for research and teaching purposes, but the Department of Public Health concluded that Berkeley’s project does not fit these exemptions due to the potential for medical interpretation.

The university’s collection of genetic samples targets only three genes: metabolism of folate, tolerance of lactose and metabolism of alcohol. Jasper Rine, UC Berkeley professor of genetics, genomics and development, said the gene variants are innocuous.

“We considered all possible misuses of this information,” he said. “We decided we could manage the risk that a student could learn that they have an upset stomach when they drink milk.”

[…]“It opens up a whole lot of questions,” [Schlissel] said. “Who has the authority to tell an individual what they’re allowed to know about themselves?”

As a geneticist, this is an interesting situation to me. If I was a UC Berkeley freshman, I would be extremely disappointed. One, I’m a genetics nerd – I’d love to know what my variants were! Two, I was told I was getting personal results – maybe I wouldn’t have participated if I would have known it was aggregate data. Three, this was completely voluntary and testing innocuous traits. If I want to know this about myself, I think I have to right to know.

But on the more general topic of genetic testing, we’re right to be wary. Personal genomics relies a lot on incomplete data and probability. Vary rarely do you have a specific gene variant that results in a certain trait or disease 100% of the time. More likely, a certain variant will say you have a 20% more likely chance of suffering from heart disease, or 35% less chance of having diabetes. That and genomics is a very new field – you may have an allele that greatly increases your risk for a certain disease, but a researcher just hasn’t discovered that yet. Does having that false sense of security negatively affect how you act?

I’m eager to get my personalized genome once I can actually afford it (so, it may not be for a while). As a geneticist, I understand how to interpret the probabilities and uncertainties, and the knowledge I get in return is worth it. But the concern is that many people who rush to sequence their genome don’t understand the probabilities, and no one is there to help them. Companies will happily sequence your genome (read: Take your money), but rarely do you have a genetic counselor there to explain the results.

Is the UC Berkeley project quite as dangerous as learning about heart disease, diabetes, and Huntington’s disease? Not exactly – they were testing for traits you probably would have already known about. Most of us are aware if we’re somewhat lactose intolerant or not as able to metabolize alcohol (you may know it as the “Asian” alcohol flush reaction). But these are concerns I’m sure we’re going to be hearing a lot more of in the future, as genetic testing becomes more and more prevalent.

I have my first scientific publication!

My first scientific paper has been published! “Allelic recharge in populations recovering from bottleneck events” by Joseph D Busch, Jennifer McCreight, and Peter M Waser. It’s included in the new book developed by the Department of Forestry and Natural Resources at Purdue University, Molecular Approaches in Natural Resource Conservation and Management:The book was actually released in June, but somehow I missed it. Just found out today because my professor gave me a copy as a going away present.

I guess I’m officially a scientist now. Woohoo!

On “fixing the gays” and science used for evil

This is old news by now – it broke while I was out of town at a conference – but enough people have emailed me asking for my opinion that I still wanted to comment. tld;dr: A researcher is giving pregnant women experimental hormones to prevent lesbianism and “abnormal” female behaviors such as aggressiveness, a disinterest in girls toys or becoming mothers, or wanting masculine jobs. Here’s the full story for those of you who haven’t heard of this yet; the rest of you can feel free to scroll past this quote to read my comments:

The majority of researchers and clinicians interested in the use of prenatal “dex” focus on preventing development of ambiguous genitalia in girls with CAH. CAH results in an excess of androgens prenatally, and this can lead to a “masculinizing” of a female fetus’s genitals. One group of researchers, however, seems to be suggesting that prenatal dex also might prevent affected girls from turning out to be homosexual or bisexual.

Pediatric endocrinologist Maria New, of Mount Sinai School of Medicine and Florida International University, and her long-time collaborator, psychologist Heino F. L. Meyer-Bahlburg, of Columbia University, have been tracing evidence for the influence of prenatal androgens in sexual orientation…. They specifically point to reasons to believe that it is prenatal androgens that have an impact on the development of sexual orientation. The authors write, “Most women were heterosexual, but the rates of bisexual and homosexual orientation were increased above controls . . . and correlated with the degree of prenatal androgenization.” They go on to suggest that the work might offer some insight into the influence of prenatal hormones on the development of sexual orientation in general. “That this may apply also to sexual orientation in at least a subgroup of women is suggested by the fact that earlier research has repeatedly shown that about one-third of homosexual women have (modestly) increased levels of androgens.” They “conclude that the findings support a sexual-differentiation perspective involving prenatal androgens on the development of sexual orientation.”

And it isn’t just that many women with CAH have a lower interest, compared to other women, in having sex with men. In another paper entitled “What Causes Low Rates of Child-Bearing in Congenital Adrenal Hyperplasia?” Meyer-Bahlburg writes that “CAH women as a group have a lower interest than controls in getting married and performing the traditional child-care/housewife role. As children, they show an unusually low interest in engaging in maternal play with baby dolls, and their interest in caring for infants, the frequency of daydreams or fantasies of pregnancy and motherhood, or the expressed wish of experiencing pregnancy and having children of their own appear to be relatively low in all age groups.

In the same article, Meyer-Bahlburg suggests that treatments with prenatal dexamethasone might cause these girls’ behavior to be closer to the expectation of heterosexual norms: “Long term follow-up studies of the behavioral outcome will show whether dexamethasone treatment also prevents the effects of prenatal androgens on brain and behavior.

In a paper published just this year in the Annals of the New York Academy of Sciences, New and her colleague, pediatric endocrinologist Saroj Nimkarn of Weill Cornell Medical College, go further, constructing low interest in babies and men—and even interest in what they consider to be men’s occupations and games—as “abnormal,” and potentially preventable with prenatal dex:

Gender-related behaviors, namely childhood play, peer association, career and leisure time preferences in adolescence and adulthood, maternalism, aggression, and sexual orientation become masculinized in 46,XX girls and women with 21OHD deficiency [CAH]. These abnormalities have been attributed to the effects of excessive prenatal androgen levels on the sexual differentiation of the brain and later on behavior.” Nimkarn and New continue: “We anticipate that prenatal dexamethasone therapy will reduce the well-documented behavioral masculinization…”

It seems more than a little ironic to have New, one of the first women pediatric endocrinologists and a member of the National Academy of Sciences, constructing women who go into “men’s” fields as “abnormal.” And yet it appears that New is suggesting that the “prevention” of “behavioral masculinization” is a benefit of treatment to parents with whom she speaks about prenatal dex. In a 2001 presentation to the CARES Foundation (a videotape of which we have), New seemed to suggest to parents that one of the goals of treatment of girls with CAH is to turn them into wives and mothers. Showing a slide of the ambiguous genitals of a girl with CAH, New told the assembled parents:

“The challenge here is… to see what could be done to restore this baby to the normal female appearance which would be compatible with her parents presenting her as a girl, with her eventually becoming somebody’s wife, and having normal sexual development, and becoming a mother. And she has all the machinery for motherhood, and therefore nothing should stop that, if we can repair her surgically and help her psychologically to continue to grow and develop as a girl.”

In the Q&A period, during a discussion of prenatal dex treatments, an audience member asked New, “Isn’t there a benefit to the female babies in terms of reducing the androgen effects on the brain?” New answered, “You know, when the babies who have been treated with dex prenatally get to an age in which they are sexually active, I’ll be able to answer that question.” At that point, she’ll know if they are interested in taking men and making babies.

In a previous Bioethics Forum post, Alice Dreger noted an instance of a prospective father using knowledge of the fraternal birth order effect to try to avoid having a gay son by a surrogate pregnancy. There may be other individualized instances of parents trying to ensure heterosexual children before birth. But the use of prenatal dexamethasone treatments for CAH represents, to our knowledge, the first systematic medical effort attached to a “paradigm” of attempting in utero to reduce rates of homosexuality, bisexuality, and “low maternal interest.”

Women like me are doomed if this process A) works and B) becomes widespread. It’s hard not to take it personally when I have every attribute they say is “abnormal” for a female:

  • Masculine career choice: Check. Science has been and is a male dominated field. I guess these drugs are to keep it that way.
  • Aggressiveness: Check. You don’t need to know me that well to figure that out.
  • Bisexuality: Sort of check. Let’s just say while I’m significantly more attracted to men, I’m still probably not straight enough for the people doing this research.
  • Abnormal peer association: Check. As a kid I had almost exclusively male friends. I did not relate to girls at all, and of the female friends I have now, most have the attributes of this list.
  • Low interest in playing with dolls: Check. I hated girly toys as a kid. Screw Barbie, give me some Legoes!
  • Low interest in caring for infants: Check. As cute as my nephews are, when they were babies I feared breakin
    g them and had no interest in feeding them or changing their poopy diapers.
  • Less frequent daydreams about pregnancy & marriage: Check. I’m supposed to daydream about these things? If anything I have nightmares about getting pregnant.
  • Less interest in having children: Check. I want a kid, but not desperately or any time soon. Maybe in my thirties, or maybe not.
  • Less interest in traditional housewife role: Check. Uh, fuck no.

It’s one thing to have society pressuring you into heteronormative roles…but now people want to alter our biology to ensure it? What is this, Brave New World? If anything we need more aggressive women who are willing to speak up instead of feeling condemned to a life as a baby making machine. If you want to have children or be a housewife, that’s fine – but it should be your choice, not forced upon you by society or hormones you did not consent to.

Knowing the views of my typical blog reader, I’m going to assume we can all agree that wanting a masculine job or not wanting kids aren’t life threatening traits that need to be corrected. I’m also going to hope that we can agree that bisexuality and lesbianism don’t need to be fixed either, as they are not a disease or harmful to anyone.

But why are we trying to fix CAH? When PZ covered this topic, he mentioned that CAH is “a real and serious disease.” The only major symptoms other than behavioral and physical masculinization are vomiting and hypertension, both which are regularly treated with supplements. Researchers and doctors are going out of their way to fix behaviors through hormones and restructure genitalia through surgery simply to make them fit into society’s stereotypical gender roles.

If anything, conditions like CAH show that nature does not always create perfectly binary males and females. Why are we altering and mutilating baby girls without their consent to make them conform to our ideal of the female figure? It’s not limited to this study – not long ago we also heard about people at Cornell who were surgically decreasing the size of young girls’ clitorises to make them more “natural.” Nothing is biologically or functionally wrong with their genitals – we decided to label them as “wrong” because of our own cultural biases.

Now, I don’t blame science for this. As a scientist, I do find it interesting that an excess of prenatal androgens can apparently alter life long behaviors. But I do have a problem when people abuse scientific findings to fit their own political or ideological agenda. Just because science finds out we can do something doesn’t mean we should do it. But humans are humans, and it seems like these abuses are somewhat inevitable.

That honestly worries me. For example, I’ve always been interested if there’s some genetic component to homosexuality, since we have overwhelming evidence that it’s biological in some way. Are there certain genes? Certain epigenetic differences? Copy number variation? Or is it all hormonal, like this study may suggest? I’m interested out of pure scientific curiosity. It’s an interesting human behavior to me, and I want to learn more about it.

But what if I did find something? As a huge gay rights activist, it would absolutely kill me to see my research findings abused in any way. I don’t want to see companies producing genetic tests for certain “gay gene”s so people can selectively abort gays. I don’t want it used to out people. I don’t want little kids screened so they can have their behaviors forcibly altered early on. There are so many horrible things that could come out of it. I personally don’t think the cause(s) of homosexuality change how we should treat it (with acceptance), but not everyone thinks like I do.

So do we avoid this research altogether? I’d argue no. We can figure out the genes that contribute to skin color without it automatically leading to more racism. We can engineer bacteria to synthesize useful materials without it automatically leading to biological weapons. What we do need to do is make sure ethics and laws keep up with the advancement of science so findings can’t be abused. But even ethics boards are made up of humans, and humans have their biases. Too many people would find nothing wrong with the studies in this post, including some people on review boards. We need to hold these people to higher standards.

It’s bad enough that these studies are harming children with no real idea of what effects it’ll have on them when they’re adults. But it’s also a shame that these studies give science a bad name – the image of a manipulative, powerful overlord found too often in SciFi novels. We must remember that science itself is neither good nor evil; the blame lies with people who abuse it.

Making a biological child for gay couples

“Is there a way to have two people of the same sex have a kid who is biologically related to both? (Either gay or lesbian couples)”

Short answer: Yes! But it’s complicated.

Long-ish answer: Creating a child from same-sex parents isn’t as easy as just combining the DNA from two eggs or two sperm. The main problem is genetic imprinting, where gene expression is modified epigenetically. That just means the actual sequence isn’t changed, but something else is edited, like adding methyl groups or modifying histones (the proteins that help wind up DNA).

And depending on if you’re a mother or a father, you genetically imprint your gametes differently. And since you generally need one functioning copy of these select genes, it doesn’t help to have two female or two male versions where they’re both turned on or off (too much or too little can both be harmful).

While that seems impossible to overcome, science is pretty impressive. Researchers have already overcome this in mice, where two egg cells were used to produce fatherless mice. So yes, it has been done in another animal!

However, who knows when or if we’ll ever see it in humans. There are always ethical concerns when you’re dealing with human subjects, and it’s hard to predict if offspring would be completely healthy using this method. I think you’d have a hard time getting this past a review board since it’s not a necessary medical procedure – same-sex couples don’t need biologically related children, even if it would be nice. But, you never know.