Should he have done more?

Here’s an interesting problem in bioethics: a person knows the field, and has an appropriate response to an individual making a serious ethical lapse, but he doesn’t report it to other authorities. Should he have?

He Jiankui, the Chinese researcher who used CRISPR techniques on human embryos, shared his ‘success’ in emails to Craig Mello, a Nobel-prize winning biologist, who then replied a few times with regret.

“I’m glad for you, but I’d rather not be kept in the loop on this,” Mello wrote, according to the AP.

“You are risking the health of the child you are editing… I just don’t see why you are doing this. I wish your patient the best of luck for a healthy pregnancy.”

“I think you are taking a big risk and I do not want anyone to think that I approve of what you are doing,” wrote Mello, who didn’t reply to a request for comment from the AP.

“I’m sorry I cannot be more supportive of this effort, I know you mean well.”

Good for Mello that he was immediately aware of the problematic nature of the research. I think my response would involve a lot more ALL CAPS sentences and a heavy use of exclamation points, and probably some profanity, but then, I’m not a Nobel-prize winning scientist. I would have also said confidentiality be damned, and contacted a swarm of other scientists and the major scientific societies and given the heads up, with a suggestion that everyone ought to be prepared to make a statement on this kind of genetic manipulation when it finally goes public. Maybe Mello did make some quiet notifications to a select few, the article doesn’t say, but it does mention this:

Mello didn’t go public with the revelation – and stayed on as an adviser to He’s company until news broke about the controversial experiment.

Yikes. He’s company. Because of course every biomedical advance must be coupled to a mechanism for extracting profit from it. That’s a great big fat bioethical problem lurking under everything.

The most disturbing news yet

Insect populations are crashing.

“We knew that something was amiss in the first couple days,” said Brad Lister. “We were driving into the forest and at the same time both Andres and I said: ‘Where are all the birds?’ There was nothing.”

His return to the Luquillo rainforest in Puerto Rico after 35 years was to reveal an appalling discovery. The insect population that once provided plentiful food for birds throughout the mountainous national park had collapsed. On the ground, 98% had gone. Up in the leafy canopy, 80% had vanished. The most likely culprit by far is global warming.

Look at these numbers.

The Puerto Rico work is one of just a handful of studies assessing this vital issue, but those that do exist are deeply worrying. Flying insect numbers in Germany’s natural reserves have plunged 75% in just 25 years. The virtual disappearance of birds in an Australian eucalyptus forest was blamed on a lack of insects caused by drought and heat. Lister and his colleague Andrés García also found that insect numbers in a dry forest in Mexico had fallen 80% since the 1980s.

Data on other animals that feed on bugs backed up the findings. “The frogs and birds had also declined simultaneously by about 50% to 65%,” Lister said. The population of one dazzling green bird that eats almost nothing but insects, the Puerto Rican tody, dropped by 90%.

Lister calls these impacts a “bottom-up trophic cascade”, in which the knock-on effects of the insect collapse surge up through the food chain.

“I don’t think most people have a systems view of the natural world,” he said. “But it’s all connected and when the invertebrates are declining the entire food web is going to suffer and degrade. It is a system-wide effect.”

Exactly. We are part of a complex web of interdependencies, and it’s also a non-linear dynamical system. There’s a word for when parts of such a system show a pattern of failure: it’s called catastrophe. By the time you notice it, it’s too late to stop it.

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.

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 maked a video

I’ve been naughty. I haven’t been keeping up with my intended schedule of one video per week. But finally I got something done.

There have been lots of distractions, but honestly? This is tough for me. There are days I don’t want to look at my face or hear my voice, and making these videos compels me to sit down and wrestle with my lack of charisma. I’ll keep plodding along, mainly as therapy — I do enjoy the process, it’s just that final step of subjecting it to the eyeballs of the world that is hard.

Oooh — “super blood wolf moon” coming

Check it out, lunar eclipse on Sunday night over a big chunk of the Earth.

The lunar event will last about four hours, beginning at 9:36 p.m ET Sunday, Jan. 20 and ending about 1:50 a.m. ET Monday, Jan. 21. The beginning of the total eclipse phase will occur at 11:41 p.m. ET, according to NASA. The duration of totality will be 62 minutes.

Unfortunately for me, we’re predicted to have a couple of days of snow around that time. Question: if the sky is socked in with gray clouds everywhere, do I still get to turn into an extra-large, extra-vicious werewolf that night?

You had just one job, Chinese space botanists

I’m not so good with keeping plants alive and healthy (one could argue I have the same problem with spiders), but as it turns out, Chinese space scientists are just as bad.

One day after China announced it grew the first plants on the Moon, the fledgling plants have been pronounced dead. Rest in peace, lunar sprouts.

On Tuesday, China’s space program said that cotton seeds had germinated in a biosphere carried to the Moon by the nation’s Chang’e-4 lunar lander. By Wednesday, mission leads had broken the news that the plants perished as the lunar night fell over the probe’s landing site.

To be fair, they are facing conditions worse than Minnesota.

The Sunday arrival of the lunar night, which lasts 14 days, deprived the plants of sunlight. During a lunar night, temperatures can plummet as low as −170°C (−274°F). Meanwhile, daytime temperatures on the Moon can reach a sweltering 127°C (260°F). These massive fluctuations are one of the main obstacles encountered by lunar explorers.

But still, that’s no excuse — they knew all this way ahead of time when planning the experiment. Were they just hoping for a spell of warm weather? They knew that wasn’t going to happen, either. Meteorology on a dead planet with virtually no atmosphere is a much easier problem than it is here.

The remaining seeds and fruit fly eggs contained in the mission’s biosphere are not likely to be viable after two weeks of light deprivation and freezing temperatures. According to China’s National Space Administration, they will decompose and remain sealed to avoid contaminating the lunar surface.

They killed fruit flies, too? I don’t understand the point of this experiment if the chamber environment was so poorly planned that one night of expected temperatures was going to kill everything.

Keep this in mind next time you read The Martian. That book was gratingly optimistic and unrealistic about everything.

Trying to figure out why this spider appeals to me

I think it’s the idea of living in your home for 16 years and never leaving it except for brief forays to leap out, kill, and eat passers-by.

I still have questions, though. What about sewage? How do they clean up the spider poop that accumulates? Also, they show a spiderling … are males more prone to wandering from home? How do they avoid getting eaten when they tap on the turret door?

Spider update

First, the bad news. I now have no adult males, because Xena ate her consort, as I feared she would. I am beginning to suspect that she’s one of those radical feminist lesbian spiders who is going to kill every male she encounters. I don’t know if they successfully mated before the murder, and she hasn’t yet produced an egg case.

Also, one of my second generation spiders, a young female, abruptly died. Before she curled up and expired, though, she did produce an egg case, so maybe her line will live on.

The good news is that right now I am keeping an eye on three egg cases. The next few weeks will tell if can keep any spiderlings alive any more.

I hope I live to be 90 before all of my sins catch up to me

James Watson, 90, has had all of his honors from Cold Spring Harbor revoked. It turns out that documentary on PBS had quite an impact.

Cold Spring Harbor Laboratory (CSHL) unequivocally rejects the unsubstantiated and reckless personal opinions Dr. James D. Watson expressed on the subject of ethnicity and genetics during the PBS documentary “American Masters: Decoding Watson” that aired January 2, 2019. Dr. Watson’s statements are reprehensible, unsupported by science, and in no way represent the views of CSHL, its trustees, faculty, staff, or students. The Laboratory condemns the misuse of science to justify prejudice.

When Dr. Watson expressed offensive views in 2007, CSHL’s Board of Trustees took immediate action to relieve him of all administrative duties at the Laboratory and terminated his status as Chancellor. Dr. Watson has not been involved in the leadership or management of Cold Spring Harbor Laboratory for more than a decade and he has no further roles or responsibilities at CSHL. In response to his most recent statements, which effectively reverse the written apology and retraction Dr. Watson made in 2007, the Laboratory has taken additional steps, including revoking his honorary titles of Chancellor Emeritus, Oliver R. Grace Professor Emeritus, and Honorary Trustee.

Lucky Jim’s luck has run out at last.