Algorithms are only magical oracles if you don’t understand them

I saw a lot of news flashes about twins comparing DNA testing services and finding that they weren’t perfectly identical, and that the services didn’t produce identical results. I didn’t bother to look any deeper, because yes, identical twins do have a small number of genetic differences, and those testing services don’t sequence your genome, they rely on chips to identify some short sequences from a subset of your genome, and there is naturally some sampling error in the process. So this shouldn’t be a surprise.

Fortunately, Larry Moran explains the sources of error.

The main problem by far is due to the way the tests are done which is by hybridizing the customers’ DNA to DNA on a microchip and reading the chip to see if there’s a match. (Ancestry.com uses the latest Illumina microchip that assays 700,000 SNPs.) I think the rate of false positives is quite low but the rate of false negatives is about 2% according to 23andMe. The absence of a match where there should be one can be due to bad luck and differences in the threshold level of binding that constitutes a “hit.” It’s these “no-reads” that makes up most of the false negatives. Because of these limitations of the assay the twins’ DNA results could differ by 2-4% of the SNPs being tested.

So no surprise that they reported some variation. What I found odd is that anyone found this odd at all.

The different testing services also reported different patterns of ancestry. Why would anyone find that to be unexpected?

While he can’t say for certain what accounts for the difference, Gerstein suspects it has to do with the algorithms each company uses to crunch the DNA data.

“The story has to be the calculation. The way these calculations are run are different.”

Heh. I believe I’ve mentioned this very point here: that saying something is an “algorithm” doesn’t mean it’s bias-free. The inputs and the weights on the data and the processing used are all choices by the person who designed the algorithms, and different companies will have different pools of data they are drawing on to make their decisions. Some people don’t get that, though.

This should be used as a nice example of how datasets and algorithms can color the interpretation of data. Maybe we’ll see fewer asshats buying into digital reductionism, as if everything that comes out of a computer is inarguable truth.

Red Hats = “malevolent, murderous goblin”

From Alyssa Milano:

Last week, a group of boys engaged with a Native American man beating a tribal drum. The exchange was caught on video. And watching that video, each of us saw what we wanted to see. Because the divisions in this country are so deep they’re fossilized.

Still, some things in that video cannot be disputed–no matter what angle or how extended the cut is. These boys, who attend a religious school, were there on a school trip protesting against a woman’s right to reproductive freedom. Several of these boys were wearing red MAGA hats, a hat that has become synonymous with white nationalism and racism. Several were doing a “tomahawk chop.” Several were laughing.

When I saw that video, I saw boys flaunting their entitlement and displaying toxic masculinity. It seemed to me like they were reflecting the white nationalism and racism that the hats on their heads have come to represent.

I sent out a tweet that read, “The red MAGA hat is the new white hood.” Right-wing pundits and anonymous trolls alike screamed for my head–literally and figuratively. My husband received death threats on his cell phone. Many demanded an apology.

Here’s the thing: I was right.

Yeah, she was. It’s so obviously true that those hats have come to represent a deep political division in this country that I’m surprised any of the right-wingers are complaining — they should just own their shit. Of course that hat represents bigotry and narrow-mindedness and tribalism and know-nothingness and American provincialism, that’s how Trump got elected. When you see someone wearing that hat, you know from the get-go they’re not going to advocate for tolerance and progressivism, that they despise immigrants, want women to get back in the kitchen and have babies, and have a deep affection for jingo and Fox News.

But I guess the Red Hats at least still have a vestige of shame if they’re trying to lie about their associations.

Oddly enough, red hats have another meaning: The redcap (or Redcap) is a type of malevolent, murderous goblin found in Border folklore. He is said to inhabit ruined castles along the Anglo-Scottish border, especially those that were the scenes of tyranny or wicked deeds, and is known for soaking his cap in the blood of his victims. Seems appropriate.

The greatest trick the devil ever pulled was convincing the world to pay him lots of money & ignore the lives he ruined

Another celebrity gets outed as a rapist and abuser. The Atlantic has posted a long expose, revealing all the rottenness that is Bryan Singer.

Almost from the moment his star began to rise, Singer, who is now 53, has been trailed by allegations of sexual misconduct. These allegations were so well known that 4,000 students, faculty members, and alumni at the University of Southern California had signed a petition asking the school to take Singer’s name off one of its programs, the Bryan Singer Division of Cinema and Media Studies—which the school did immediately after Sanchez-Guzman filed his suit. As one prominent actor told us, “After the Harvey Weinstein news came out, everyone thought Bryan Singer would be next.”

Everyone with power in Hollywood has known this for 20 years. Yet still he kept getting work.

The portrait of Singer that emerges is of a troubled man who surrounded himself with vulnerable teenage boys, many of them estranged from their families. Their accounts suggest that Singer didn’t act alone; he was aided by friends and associates who brought him young men. And he was abetted, in a less direct way, by an industry in which a record of producing hits confers immense power: Many of the sources we interviewed insisted, out of fear of damaging their own career, that we withhold their name, even as they expressed dismay at the behavior they’d witnessed.

Oh, I am so dismayed. May I bring you another teenage boy, Mr Singer, sir? How about a multi-million dollar movie contract?

It seems we have a system in which the worst people in the world can thrive, and nothing holds them in check. Maybe, in addition to the actual culprits themselves, some of these anonymous cowards and chickenshit enablers need to be dragged into the light, too.

The hypocrisy of Boghossian’s academic defenders

I was listening to the latest Serious Inquiries Only podcast, on the Boghossian affair, while I was pumpin’ iron down at the gym, and Eli Bosnick made a really, really good point. After reading these various serious statements of support for Boghossian from people like Richard Dawkins and Steven Pinker — they’re piously declaring that demanding he follow IRB requirements is a threat to academic freedom — he mentioned a curious omission. While they rush to the defense of their alt-right, Intellectual Dork Web colleague who has violated university policy and faces a rebuke from the university administration, they’ve never said a word about…Turning Point USA.

You know TPUSA is a Koch-funded far-right organization that trains students to incidents at universities so they can get left-leaning professors fired. They’re kind of incompetent at it — wearing diapers to show that left-wingers are babies isn’t very impressive — but you still don’t get to accuse universities of Orwellian behavior when right there, right in front of their faces, with no apologies and forthright insistence, TPUSA is maintaining an Orwellian Professor Watchlist (fair notice: I’m on it).

On the one hand, you’ve got a university calling in bigoted anti-feminist employee to a meeting (oh god, that’s torture!) because he violated university policy; on the other, a well-funded right-wing organization making an enemies list of professors and encouraging action against them. Which one do you side with? It says a lot about you.

What do biologists really think of sex and gender?

I was recently berated by someone telling me that they were surprised that a biologist, who does things like determining the sex of a fly, a fish, or a spider, actually agrees with people who see gender as fluid and variable, and not necessarily in alignment with sex. All I can say is…there are an awful lot of people out there with a seriously mangled version of scientific concepts. Worse, they use their misunderstanding of basic terms to argue that they have a scientific foundation for their bad ideas.

Just to help you out, here’s a succinct definition of some fundamental concepts, as written by an ecologist in the PLOS Ecology Community blogs. Your expectation that biologists share the narrow, bigoted views about sex and gender that you have are probably totally wrong — so you might want to hesitate next time you think it’s a good idea to lecture professional biologists on biology.

The words “sex” and “gender” are often used interchangeably in colloquial contexts, but they have different meanings that are relevant to our work in ecology.
“Sex” refers to categories based on a combination of biological and physical characteristics, such as body organs, chromosomes, and hormones (WHO 2011, APA 2015). Sex is commonly assigned on the basis of external genitalia at birth and is often assumed to be only male or female, but scientists have identified at least five different groupings of human sex chromosomes, anatomy, and hormone physiology (Fausto-Sterling 1993). Other terms that relate to sex include intersex, freemartin, and hermaphrodite. (Note that hermaphrodite is a term currently used for animals but considered outdated and rude when used to describe humans; the preferred contemporary term for humans is intersex.) (“Sex” can also refer to activity among one or more individuals that may or may not result in sexual arousal and/or genetic recombination. I’m not addressing this meaning of the word in this piece.)
“Gender” refers to identities and categories based on social or cultural characteristics (WHO 2011, APA 2015). Gender is both internal (gender identity, which is each person’s innate sense of their own gender), and external (gender expression, which is how each person expresses their gender identity). Woman, man, masculine, and feminine are all terms that can refer to gender. Transgender is a term used to describe a person whose gender identity is different from the sex they were assigned at birth. Gender is primarily a human and social term, and it is not usually relevant for non-human animals or plants.
When we observe biological and physical aspects of our study organisms, those observations tell us about the sex of those individuals, not the gender.
When we interact with other humans, we usually know more about their gender rather than their sex: for example, we often know about their clothing and hairstyles but not very much about their body organs, chromosomes, or hormones. (Furthermore, and this fact may be obvious, but clothing and hairstyles are not necessarily signifiers of any particular gender identity.) Among humans, sex and gender may be related, but they are not equivalent. In other words, female and woman are often thought to be synonymous, but in reality, female refers to different characteristics than woman does.

Also good was this bit:

If you (a) are talking about scientists and (b) interested in categories such as “women” and “men,” it’s more polite to use gender rather than sex categories. Why? In professional contexts, we may think we know what gender our colleagues present themselves as (e.g., women, men), but probably don’t know very much about the biological sex of our colleagues (e.g., chromosomes, body organs, hormones). It’s odd and inappropriate to make assumptions about other people’s bodies, especially in a professional context.

This. When I meet people, I don’t know anything about their sperm count or their chromosome arrangement or even what their genitals look like (you don’t have to show me), so all the sex details are irrelevant to our interactions. Gender matters because we have a huge amount of social capital, some good, some bad, invested in how people present themselves, and also because those gender signifiers are diverse and do a better job of reflecting how people see themselves in society, and how society sees them.

You know, when a population is identified as a discrete binary of two kinds of individuals, male and female, my usual thought is that the next step is to pair up individuals in bottles and do a genetic cross. That’s not how we treat human beings in our communities.

I think we can safely say #gamergate is dead

It wasn’t that long ago that being a gamer meant you were a regressive asshole. Here’s the segment of hbomberguy’s long twitch stream in which Alexandria Ocasio-Cortez shows up to talk about the importance of trans rights while the gamer bounces a gorilla around the screen. I know, that part seems weird, but hey, AOC is taking this opportunity to make a clear statement, so you can’t complain.

I have no idea what’s going on on the screen, but the words make sense.