Nineteen days later: How gay are you?
November 25, 2019 1:55 PM   Subscribe

How Earnest Research Into Gay Genetics Went Wrong. When a well-intentioned study led to a dubious DNA test for same-sex attraction, it exposed the need for safeguards on research in the age of big genetic data.
posted by sciatrix (27 comments total) 20 users marked this as a favorite
There is already an issue of commercially available DNA tests potentially outing trans people. Generally Y haplogroup is only displayed for people with Y chromosomes, so one might infer that people who display their gender as female who show a Y haplogroup may be AMAB, though 23andMe can display that information based on the person's father also being tested by the site.
posted by larrybob at 2:35 PM on November 25, 2019 [2 favorites]

Yeah, that's also an issue for intersex people as well as trans people. My genetics lab has begun doing some basic genome sequencing that allows students to extract and sequence their own DNA in the lab at some neutral loci used primarily for DNA fingerprinting and paternity analysis in the past year. I was rather pleased when my instructor made the decision to simply exclude the X chromosome-linked marker included in the kit from group analysis on the theory that there's no good reason to draw attention to a student's sex chromosomes in a class of the student's peers.
posted by sciatrix at 2:40 PM on November 25, 2019 [39 favorites]

Those systems revolve around research subjects—the people who consent to getting poked and prodded and experimented upon. But what happens when the people who are the potential victims of research are not the people who are giving the samples?

This seems to be the crux of the matter, as also seen e.g. in cops' abuse of genealogy databases.

It seems like what the article calls "subjectless science" would necessarily require a subjectless ethics -- an ethics that moves beyond the convenient fiction of the self. Can any of our resident bioethicists shed light on whether that is a thing that is happening?
posted by Not A Thing at 2:40 PM on November 25, 2019 [2 favorites]

trying to pin social construction and identity manifestation on the existence of a set of genes seems to totally miss the point of what social construction and identity manifestation is. Unless what we want is to build a social construct around DNA as a eugenicist/evopsych "biological fact" that is then used to create a permanent authoritarian regime of biological control over all human life and this is where I get too sketched out and need to go back to OkCupid to find more poly gay trans cuties to kiss on.
posted by nikaspark at 2:51 PM on November 25, 2019 [8 favorites]

To me the obvious bad science here is that what "gay" means is very complicated. You could ask a much narrower question, like "if you are a cis-man have you had sex with another cis-man in the last year". But even that's still subjective (what is "sex" exactly). For something so fraught as sexual identity there's just not a good simple phenotypic identifier.

But in the world of genetic research right now I'm worried about a much simpler mathematical problem. The quality of the statistics.

Right now the world is full of assertions like SNP Rs1042725 results in 0.35 cm extra height in men. There's a lot of these height SNPs, and the naive problem wtih them is if you add them all up someone with the perfect genome would be fifteen feet tall. Clearly there's some convolution or other biological factors at work, it's not a simple linear relationship.

The deeper problem is this kind of genetics research relies on very subtle statistics, teasing a signal out of a very noisy dataset. It's not quite as dumb as, say, p-hacking but it's not a lot better either. Combine the risk of dodgy statistics with really bad phenotypic classification and you end up with total garbage.
posted by Nelson at 2:52 PM on November 25, 2019 [13 favorites]

Joel Bellenson, began with: “A new study published in Science, on 29 August, and based on the genomes of nearly 500,000 people, has blown up the simplistic expectations of a single gene for same-sex attraction.” He went on to make some bizarre claims that perhaps the discrimination LGBTQ+ people suffer is “crucial for their fullest intellectual and social development,” comparing the creative prowess of “the Alphabet people” to the genius Jews are said to have acquired through enduring generations of oppression and genocide.

Neale says he and his coauthors were still discussing a course of action when Vitti launched his petition. He was tempted to ignore [the app], in the hopes it would go away.

Fuck them both. This and similar have basically taught me that the academy is fundamentally untrustworthy.
posted by PMdixon at 3:32 PM on November 25, 2019 [1 favorite]

All of which seems to put researchers like Neale in an impossible bind. If the data is out there, someone will do the science. And if the science is out there, someone will warp it to their own commercial or ideological agenda. Which is why bioethicists like Holly Lynch, at the University of Pennsylvania, think it’s time to reconsider whether existing ethical frameworks go far enough to protect people who aren’t the subjects of research themselves.

The data is out there.

A very X Files sound byte(sic). My crazy proposal, we need a Zeroth Amendment that protects the individual from technology. Without total reversion to a pre-tech world the data will be out there in many repositories, forever. We need to protect people but use the data to improve the world. (the amendment kinda needs to be not just international but soon solar system wide and much stronger than the first amendment)
posted by sammyo at 4:05 PM on November 25, 2019 [1 favorite]

When Neale’s team tried to use the genetic markers they’d found to predict how people in unrelated data sets reported their sexual behavior, they found almost no correlation.
Doesn't this mean that they thought they found something, but then it turned out that they didn't?
posted by clawsoon at 4:30 PM on November 25, 2019 [3 favorites]

There is already an issue of commercially available DNA tests potentially outing trans people.

That link is actually way more than I hoped for. I knew that you had to out yourself to them for the results to compute, but, with the caveat that I'm the sort of person, even were I not trans, I wouldn't be doing 23 and me, they've done all you could ask for short of allowing you to disable the Y haplogroup--they have said "this can out you to anyone with basic reasoning skills", which you'd hope would be obvious if you're putting your genotype on the internet.
posted by hoyland at 5:27 PM on November 25, 2019 [2 favorites]

Doesn't this mean that they thought they found something, but then it turned out that they didn't?

Not necessarily. This is an oversimplification, but it's essentially Bayes' Rule: the probability that a person has a certain gene given that they have sex with members of the same sex can be high, while the probability that the person has sex with members of the same sex given that they have that gene is low. Symbolically,

P(gene | gay) ≠ P(gay | gene)

In reality, the stats used for genome-wide association studies are much more sophisticated than that, but conceptually this still applies. You can find real, potentially interesting results in the genetics from known phenotypes, without necessarily being able to predict the phenotype from the genetics. This happens a lot, actually.

I'm sympathetic to Neale's choice to be involved in the study to hopefully guide it to a better outcome, but obviously it didn't work out as he'd hoped. The reality is that they probably needed a bioethicist or similar as a consultant on the study. Considering the social consequences and probable public interpretation of a research study is not necessarily part of the training of a geneticist. Neale clearly was concerned enough about these issues that it entered his decision process in getting involved in the study, but evidently didn't consider that addressing them appropriately would probably require expert help. Getting Out@Broad involved probably would have helped, but an actual expert in thinking about ethical, social, and political consequences of scientific research should have been recruited. Of course, while it's obvious in retrospect, if I were in his position, I don't know if I would have been forethoughtful enough to do this, either. It's a cautionary story to keep in mind.
posted by biogeo at 6:18 PM on November 25, 2019 [6 favorites]

To me the obvious bad science here is that what "gay" means is very complicated. You could ask a much narrower question, like "if you are a cis-man have you had sex with another cis-man in the last year".

For what it's worth, the specific question asked by the study was "ever versus never had a same-sex partner".

There's a lot that can be said about the ethics of this study, but I think Joe Vitti describes the most important issues pretty succinctly in his blog post, "Big data scientists must be ethicists too". Joe's twitter feed for the past week is worth reading too.
posted by grouse at 6:34 PM on November 25, 2019 [3 favorites]

Of course, while it's obvious in retrospect, if I were in his position, I don't know if I would have been forethoughtful enough to do this, either. It's a cautionary story to keep in mind.

I mean, personally, I would have been forethoughtful enough to consider the idea deeply and then not do it. Especially given the phenotypic criterion they're actually associating with the SNPs in the study, which is not identity or even necessarily orientation but rather is answers to the following question: "Have you ever had sex with someone of the same sex?" I think that with respect to certain identities and classes of people, studies of genetic basis are necessarily really fraught, in part because it is so easy for that information to be quickly leveraged in ways that can really hurt marginalized people--whether or not the SNP associations are really all that meaningful in any specific case.

That doesn't mean that there are research questions that can never be approached, but I do think that researchers working on questions like this need to get ethics and community commentary well ahead of time. Of course, the fear then would be whether or not the researchers got scooped and lost their Science paper, but that's the consequence of being careful.

I can say that I'd have thought of this really confidently because my PI (who is also gay) and I have had a number of discussions about both the ethics that must be considered when embarking on studies of human sexual orientation and also about this specific study before the GeneBank app and the widespread criticism came out. The whole story has been really frustrating for me to watch.
posted by sciatrix at 6:41 PM on November 25, 2019 [13 favorites]

Rainbows are 'pandering'?

Who are these people. Presumably the ones who think the good gays look and act like upper class white preppy peeps.
posted by liminal_shadows at 6:42 PM on November 25, 2019 [2 favorites]

The reality is that they probably needed a bioethicist or similar as a consultant on the study.

Wouldn't it be a bit more useful to consult some gay people? I'd rather have consultation with a diverse pool from the affected group than consultation with someone, probably straight, with the cultural capital needed to become a bioethicist. Even a rich white cis gay bioethicist is going to be speaking from a really different standpoint than most GLBTQ people, no matter what his training.

I really wish that people would have the humility to treat the people their research affects as valid speakers about their lives rather than as mere subjects of knowledge, and I wish that people affected by research were consulted about it rather than one individual "expert" from the upper middle class who treats the affected people as a subject of study.
posted by Frowner at 6:54 PM on November 25, 2019 [5 favorites]

Wouldn't it be a bit more useful to consult some gay people?

One of the two main coauthors, Ben Neale, is gay. So was their sociologist consultant, Robbee Weddow. I've had an awful lot of arguments with cis gay men of my acquaintance who argue very earnestly that there are no potential downsides to this kind of research and that the information acquired from these studies is very unlikely to have repercussions for anyone in queer communities. It's not as simple as "ask a gay person," unfortunately--it matters which one you ask.
posted by sciatrix at 6:59 PM on November 25, 2019 [25 favorites]

I don't feel qualified to judge whether Neale's experience as a gay man is sufficient representation on the research team, but like I said, getting Out@Broad involved earlier in the process probably would have been a good idea, as Neale acknowledged. Maybe the fact that this population is still scientists means their experience isn't sufficiently representative, but it seems that this group did actually predict problems with this work and give useful feedback, only some of which was taken.

As for whether the study should have been done at all, well, I agree that its execution is sufficiently flawed that whatever scientific value the authors hoped to get from it fails to outweigh the obvious risk of social harm. Just as you said, sciatrix, the question "Have you ever had sex with someone of the same sex?" is so weakly related to the question of what a person's sexual orientation is as to be useless. Being such a complex biocultural phenomenon, any question to operationalize sexual orientation for the purposes of a GWAS is going to have limitations, but the one they chose is particularly bad, reminiscent of the original Kinsey studies.

I don't mean to say that I can imagine myself having undertaken this particular study, which isn't in my field anyway, only that I can imagine myself undertaking a study on a different topic that has implications outside the academy while thinking that I've got a good handle on how to frame it for public consumption, while actually being totally out of my depth. There are some topics I've spent a lot of time thinking about that I would easily avoid, just as it sounds like you and your PI have, but there are others I'm sure I haven't. This just makes me think more about how I might address the problem of not knowing what I don't know when it comes to consequences of my research. There are plenty of opportunities for grad students and postdocs in my lab and department to get feedback from fellow scientists early on in the process of conducting a research project, but by the time someone from the bioethics department is likely to see someone talking about their work, the work will have already been completed. This makes me think that it could be a good idea to talk with my PI about inviting someone from the bioethics group to sit in on our weekly lab meetings.
posted by biogeo at 7:29 PM on November 25, 2019 [3 favorites]

As a bisexual trans woman who has gay sex what terms are we using to describe same sex in a way that doesn’t absolutely misgender me.

You gotta answer that question before you can find the gene otherwise you’re assuming trans, non-binary and intersex people are just temporarily embarrassed cis folk which we ain’t.
posted by nikaspark at 7:32 PM on November 25, 2019 [8 favorites]

It's not enough to have members of a vulnerable population as part of your study team. That's the group of people who get a career-boosting paper in Science on their CV.

If you want meaningful consent to work with a vulnerable population you need to get it from someone who is representative, independent from the study team, and accountable. In previous human genetics research on vulnerable populations this has often meant someone like a tribal leader. Here, getting consent from, for example, a well-known national gay advocacy group might have proven sufficient.

But what responsible group or leader, you may ask, would feel able to consent on behalf of all gay people for something that does not benefit gay people in any way? That's exactly the point.

Thanks for posting this, sciatrix. Somehow I missed that this story had finally come out. A few tweets by me on the subject begin here.
posted by grouse at 7:38 PM on November 25, 2019 [4 favorites]

Oh, and I know exactly what you mean about arguing with people who earnestly believe there are no downsides to research on {biology of homosexual attraction / biology of gender identity / biology of a psychological trait / biology of some other thing}. As scientists we tend to be biased towards seeing the positive value of any source of new knowledge, but unfortunately a lot of people seem to believe that you have to either think something is beneficial or harmful, rather than acknowledge that something can have both beneficial and harmful effects that need to be weighed together. Because they see the positive scientific value of some research question, they don't allow themselves to accept that there may be negative social costs in pursuing it. There's a lot of research that we could do that would be scientifically valuable, but has obvious negative consequences such that we shouldn't do them. Saying this here is of course preaching to the choir, but it's just so annoying running into this attitude that I have to vent a bit.

I think our ethics training as scientists is generally reasonably good at focusing on individual harm to, e.g., research subjects. Everyone on an NIH training grant is required to undergo ethics training that usually includes things like medical ethics, privacy, animal welfare, etc. I assume other funding agencies have similar requirements. But when it comes to discussion of the ethics of social impact of research? I don't know that I've ever encountered that in any of my ethics training, aside from maybe at most some vague hand waving that this is a thing to think about. There are lots of scientists who worry about these questions anyway, of course, but there are plenty who have a blind faith in the idea that scientific progress is good, therefore the social consequences of scientific research are good.
posted by biogeo at 7:46 PM on November 25, 2019 [5 favorites]

At the American Society of Human Genetics annual meeting there are always invited sessions on social issues. The year this study this post discusses was unveiled, there was one on how to work with the specific vulnerable populations of indigenous people. A lot of lessons could have been learned there that would have transferred here.

At the Biology of Genomes conference there is always a session on the ethical, legal and social implications of genomics research. Seeing how empty the room is for this session in this otherwise overstuffed conference is amazing. And also incredibly embarrassing to me as a genomics researcher.

The discussion is there for those who want it.
posted by grouse at 8:03 PM on November 25, 2019 [7 favorites]

Ha! Science is still arguing about the 'hard problem' of consciousness. Even though its really hard to do science when you're ... *unconscious*.

Oh but take something complicated like 'varieties of religious experience' and ... yeah, there's a GENE for THAT!!!

Right ....

" Science is the belief in the ignorance of experts." — Richard Feynman
posted by Twang at 8:06 PM on November 25, 2019

For what it's worth, the specific question asked by the study was "ever versus never had a same-sex partner"

...which is a profoundly bad way of measuring whether someone is gay. Like, does it not really count until you actually have sex with someone? I get needing a simple definition for research purposes but this one is so off that it seems to make this whole project garbage right from the start.
posted by augustimagination at 12:13 AM on November 26, 2019 [5 favorites]

For what it's worth, the specific question asked by the study was "ever versus never had a same-sex partner" ...which is a profoundly bad way of measuring whether someone is gay.

I'm having a heck of a time googling a citation, but I recall reading that the Wolfenden Report cited a survey of sailors finding that roughly half had engaged in sexual activity of some kind with another man.
posted by hoyland at 4:07 AM on November 26, 2019

On October 24, it changed the app’s name to “166 Shades of Grey” and removed the ability to purchase it, before scrubbing it from the site altogether, as Nature reported.

while this was the case as of 31 oct 2019, as of 26 nov 2019, references to its existence are back on the site as "122 Shades of Gray".

it's pretty noxious. CW for some shitty stuff ahead, hidden in abbr tags so hover if you want to read them or go to the link above.

paragraph 4
graph 5
graphs 12-14 are mentioned in the wired article and holy fuck
posted by anem0ne at 7:32 AM on November 26, 2019 [1 favorite]

When I hear these sort of pragmatic/utilitarian arguments that any research that can be done should/will be done and there's no reason or way to stop it, I think of hearing Stephen Pinker argue exactly that in arguing against a comprehensive set of bioethical standards for biotech research at a conference a few years ago (and seeing Margaret Atwood and a bunch of biologists completely slap down his arguments).

I hate to make a slippery slope argument, but there is something to be said for the fact that the guy who proudly argues against establishing ethical standards for biological research is also the guy who was glad to hang out with a pedophile, rapist, and child sex slave trafficker and whose evopsych arguments were used by that rapist to justify his actions.
posted by hydropsyche at 9:18 AM on November 26, 2019 [4 favorites]

The author paraphrases Neale's thinking: On the other hand, a better understanding of how genetics influences same-sex attraction could also help destigmatize it.

Why on earth should we take this claim at face value? Has understanding the genetic basis for skin color or chromosomal sex done anything to reduce racism or sexism? As a queer person I don't want or need any legitimacy conferred by ~~Science~~ to confirm that it's okay for me to live as I am. Queer and trans people aren't a problem to be solved.
posted by dusty potato at 9:56 AM on November 26, 2019 [10 favorites]

Ethics training and practice in human genetics is completely lacking. My experience as a biologist is also that we had to take one completely laughable course on ethics in grad school that was basically like, “don’t falsify data or make a humanzee.” It might be interesting to compare with related fields like anthropology and sociology, which from talking to trainees in those departments I got the sense were a lot farther along in terms of acknowledging, looking actively for, and reckoning with these types of social impact issues.
posted by en forme de poire at 11:03 AM on November 28, 2019 [3 favorites]

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