Is it progress when a self-aggrandizing mad scientist performs a reckless experiment?

Does this look like your idea of a mad scientist?

China is racing ahead in human biotechnology — it really helps when you can disregard ethical concerns altogether. It especially helps when you pay lip service to bioethics while simultaneously carrying out a major research program that directly contradicts the ethical concerns you’re piously declaiming.

There is a heroic history of scientists engaging in self-experimentation. The example that comes to mind is Barry Marshall, who drank down a solution of Helicobacter pylori to prove that the bacteria was the causal agent behind stomach ulcers. No research review committee would have approved such an experiment, but it paid off in that he won the Nobel for it. He also made himself very sick. It was a dramatic and rather stupidly dangerous gesture — there are safer ways to evaluate pathogens, and we drill safety into our students all the time.

Maybe we’re wrong. Maybe we should be encouraging students to lick random slime they find on the lab benches. We might lose a few, but the tiny percentage who discover brand new drugs or new diseases will make the deaths worthwhile, right?

But that’s self-experimentation. The new era of gene editing really is meaningless when done on yourself. It’s got to be done on embryos, on someone else. Is modifying genes in some other helpless, innocent person still heroic, or even heroically stupid? I don’t think so. We’re at the stage where experimentation on human cells is important, but the ethical guidelines don’t allow you to grow up that blastocyst to birth, because at that point you have a person who did not consent to the manipulation, and they have to live their whole life with the consequences of your tinkering.

That didn’t stop He Jiankui from launching a research program in which he genetically modified IVF embryos with Crispr, implanted them back in their mothers, and then cheerfully announced when the first of them gave birth.

There are more than a few problems with this experiment.

  • We don’t know all the limitations of Crispr yet. He assures everyone that there were no spurious modification of the genome in this case. Were there other cases, though? Do we trust that failures would be reported?

  • The entire purpose of this modification was prophylactic. They knocked out a component of the immune system that HIV uses to infect cells, presumably giving the child resistance to AIDS. Was this a pressing need? The child did not have a disease, they deleted a molecule to make it less likely they would get a disease. (The father is HIV-positive, so there was greater risk of exposure…but how much fluid transfer were the parents expecting?)

  • The deleted gene is CCR, which provides a kind of latch between T cells of the immune system and antigens. Most humans have CCR, a small percentage do not, and they have a greater resistance to some specific pathogens. But are there trade-offs? Are they more susceptible to other pathogens, or does it generally weaken the immune response? We don’t know, but hey, maybe now there will be a bunch of kids in China who will have genetically engineered weaknesses!

  • The experimenter had rushed a paper on bioethics to publication before this conference where he announced his result. The paper states that this kind of experiment is unethical.

    On Monday, He and his colleagues at Southern University of Science and Technology, in Shenzhen, published a set of draft ethical principles “to frame, guide, and restrict clinical applications that communities around the world can share and localize based on religious beliefs, culture, and public-health challenges.” Those principles included transparency and only performing the procedure when the risks are outweighed by serious medical need.

    …

    He was actively pursuing controversial human research long before writing up a scientific and moral code to guide it.“We’re currently assessing whether the omission was a matter of ill-management or ill-intent,” says Barrangou, who added that the journal is now conducting an audit to see if a retraction might be warranted. “It’s perplexing to see authors submit an ethical framework under which work should be done on the one hand, and then concurrently do something that directly contravenes at least two of five of their stated principles.”

    It’s true. Patent dishonesty ought to be a good reason to pull a paper.

  • He doesn’t seem to be particularly aware of the limitations of genetics.

    He appeared to anticipate the concerns his study could provoke. “I support gene editing for the treatment and prevention of disease,” He posted in November to the social media site WeChat, “but not for enhancement or improving I.Q., which is not beneficial to society.”

    OK, I’ll bite. What genes for “improving IQ”? It’s easy to say you won’t do experiments on a gene that doesn’t exist, or involves modifying a very large number of mostly unidentified genes. I also don’t believe him. Of course improving intelligence would be beneficial to society — we try to do that all the time, it’s called education. If he had a target gene that was associated with greater intelligence, you know he’d be recruiting volunteers to do the study right now, which he’d carry out surreptitiously until he got a positive result that he could highlight at a major conference.

  • The lack of transparency while the experiment was ongoing is deeply troubling. If you don’t let people be aware of and monitor your potentially risky experiment, it’s too easy to literally bury (or cremate) results that you don’t like. It’s like p-hacking, where in this case the “p” stands for “people”.

  • This guy is a biophysicist and bioengineer. He is not qualified or trained in any way to assess ethical risks, but heck, we all know that the magic words “physicist” and “engineer” make one all-knowing, confident, and wise. I can only dream of having the degree of certainty that would allow me to publish a paper in a complex field which I know nothing about, and where my actual work flouts everything I say others should do. But then, I’m not a physicist.

I also have to add that this is not a particularly radical experiment. Crispr is now an established technique, and these sorts of experiments have been carried out in experimental animals. The only thing novel about it is that he rushed to execute an experimental technique, developed by other, more careful scientists, on a different experimental animal, human children. I expect there will be a day when gene editing on embryos is done to improve the quality of life for human beings, but that day doesn’t seem to be here yet, and reckless experiments don’t bring it any closer.

The space people are getting busy

We have successfully invaded Mars again, this time to poke holes in it.

The InSight lander, operated by NASA and built by scientists in the U.S., France and Germany, touched down in the vast, red expanse of Mars’ Elysium Planitia just before 3 p.m. Eastern Monday.

There it will operate for the next two Earth years, deploying a seismometer, a heat sensor and radio antenna to probe the Red Planet’s interior. Scientists hope that InSight will uncover signs of tectonic activity and clues about the planet’s past. Those findings could illuminate how Mars became the desolate desert world we see today.

Oh. Practical knowledge, since we’ve got an ongoing experiment to see if we can turn Earth into a similarly desolate desert.

If you don’t want to learn about how to end all life as we know it, you could tune in here on Wednesday afternoon, when I’m getting together with some other space people, the Deep Astronomy channel, to talk about the origin of life. It’ll be fun! Space people are cool!

Spiders will just break your heart

Last Wednesday, I was so optimistic. I’d paired up Vera with a first-generation son of Gwyneth (GI-♂), they’d gone at it hot and heavy, and had produced an egg sac — an egg sac with a peculiarity I’ll get to in a moment. My plan was to go in today and open up the sac and see what embryos I’d find.

The peculiarity was that although I’d classified all my spiders as Parasteatoda tepidariorum, there was still a little uncertainty. The patterns of pigment on their cuticles were a bit ambiguous. Here’s part of the description of P. tepidariorum from Common Spiders of North America.

This is a medium-sized to large cobweb weaver. The abdomen appears teardrop shaped as the spider hangs updide down in its web, spinnerets uppermost. The cephalothorax is tan or brown. The abdomen color is extremely variable, usually shades of light brown with a mottled tan or brown. Some individuals are nearly black, others unmarked and pale. The legs are darker at the joints.
…
The egg cases of this spider are tan and tardrop-shaped, point uppermost.

This describes my spiders perfectly, given that there is variability in the patterning of the abdomen. They look different, which had me worried that I may have gathered a couple of different species, but then the description of the egg case settled it for me: Gwyneth had produced lovely tan, teardrop-shaped egg cases. Case closed, right? Gwyneth and her progeny were P. tepidariorum.

Then Vera produced an egg sac. Vera herself also fits that description of P. tepidariorum to a T.

But the egg sac she produced was a cottony, pure white ball. What? I flipped through my books looking for some indication of what this might mean, and found a description of Steatoda triangulosa, which is also common in this part of the country.

This is a medium-sized cobweb weaver. The cephalothorax is reddish brown. The legs are light brown with dark brown bands. The apdomen is light brown with two rows of angular spots or bands of dark reddish brown separated by white areas with a mottled appearance. In some individuals this pattern looks checkered.
…
The egg case is a fluffy white sphere.

Uh-oh. Are Vera and Gwyneth from two different genera? There’s nothing in Vera’s abdominal pattern that fits S. triangulosa, but maybe that’s highly variable in this species, too, and the egg case definitely fits this description. But she’d bred with P. tepidariorum! Were the new eggs hybrids? Was I just a terrible ignorant klutz playing the taxonomy game poorly? I went into the lab to take a few steps towards finding out.

And…disappointment. The “fluffy white sphere” was gone — it had been torn apart. The eggs within were dried up lumps. Uncertainty reigns.

I put the two lousy parents into a petri dish and made a video. You look and tell me: Parasteatoda tepidariorum or Steatoda triangulosa? Looking at just the adult morphology, I’m saying P. tepidariorum, but what do I know. Video below the fold, with an agitated pair of spiders scurrying about.

[Read more…]

Happy Spider Report: Vera was preggers!

It’s all good news. All the spiders are thriving right now, chowing down on flies. Vera produced a very pretty egg sac — I’m thinking the 14/10 light/dark cycle may have something to do with it — and has shrunk to about half her previous size. I’m planning to open up the sac on Sunday as part of my devotional, just to check on the health of her embryos. Although I’m low on adults, the next generation is coming along, and with any luck I’ll have a swarm of spiderlings this time next week.

The real enemies of good science

I’m still tuned in to the basal level of creationism in this country, and still keep an eye on the fools who are still making noise. But yesterday I was alerted to this new video by “Dr” Grady McMurtry titled 25 proofs the Earth is young, and I couldn’t believe it. The guy is a buffoon, he was pompously declaring the same old crap creationists have been squirting out since George Mcready Price, and I just didn’t care. Flood geology, from a guy who knows less geology than I do, are you fucking kidding me? In 2018?

The world has moved on. Those ideas are so dead that they rely entirely on surprising the media with how stupid they are to get any attention — the flat-earthers are the same way. What anti-science fantasy can we come up with that is so knuckle-draggingly idiotic, so irrelevant to the way the world works, that television crews will flock to us to put us on cable, that we’ll get mentioned in the New York Times, that will get us a big feature in an online magazine?

Sure, there are people who deeply believe — the piety of yokels is still inflating the gas-bag of creationism, and a few frauds are making bank off all kinds of absurd claims. Yeah, you can rake in the bucks and the media attention if you build a big building with a boat-like facade and claim to have the evidence for Noah’s Ark, and we should continue fighting against that (it is necessary that the religious con artists not think they can get a free pass despite lying to the public), but at the same time we should be aware that these are just the flamboyant excrescences of a rot that has a deeper and more dangerous core.

Holly Dunsworth cuts to the chase (I’ve been noticing that a lot of anthropologists are coming to the forefront in the battle against evolutionary ignorance):

Evolution educators—even if sticking to E. coli, fruit flies, or sticklebacks—must confront the ways that evolutionary science has implicitly undergirded and explicitly promoted or has naively inspired so many racist, sexist, and otherwise harmful beliefs and actions. We can no longer arm students with the ideas that have had harmful sociocultural consequences without addressing them explicitly because our failure to do so effectively is the primary reason these horrible consequences exist. The worst of all being a human origins that refuses humanity.

So many of us are still thinking and teaching from the charged tradition of demonstrating that evolution is true. Thanks to everyone’s hard work, it is undeniably true. Now we must go beyond this habit of reacting to creationism and instead react to a problem that is just as old but is far more urgent because it actually affects human well-being.

Bad evolutionary thinking and its siblings, genetic determinism and genetic essentialism, are used to justify civil rights restrictions, human rights violations, white supremacy, and the patriarchy. As a result, evolution is avoided and unclaimed by scholars, students, and their communities who know this all too well.

I still think religion is a major driver of bad science in this country, but it’s also become obvious that non-religious people — some of the atheists I used to hang out with — have found a way to become assnuggets who are just as deplorable as Christian fanatics, and the path they’ve taken to turn into corrupters of culture and science is exactly what Dunsworth describes: genetic determinism and genetic essentialism. They’ve gone from using the Bible to justify misunderstanding evolution, to using their misconceptions about genetics to justify misunderstanding evolution, and along the way, they’re revitalizing bigotry and nationalism and revisionist history. In some ways, they’re worse than creationists. Creationism is a joke, its religious underpinnings are simply too obvious. When you promote a more subtle (usually) racism and misogyny while donning the mantle of Science™, you’re more effective at fooling the moderately well-educated.

YouTube is the most obvious example of the decay in full flower. You can find plenty of delusional know-nothings like Grady McMurtry babbling away, but far more influential are the swarms of alt-right/classical liberal/centrist/whatever-the-fuck-they-call-themselves atheists and so-called skeptics who preach a purely secular version of contempt for races and sexes, while claiming they have the imprimatur of evolution. They don’t. They’re little more than 19th century bigots pretending to be scientists, busily tainting good science with fascism and Victorian nonsense.

That looks to be the next big fight, not against the dopey inheritors of Seventh Day Adventist mythology, but against the unthinking champions of 200+ year old pseudo-scientific racialist ideas.

@MrPeterLMorris demands that I explain gender and all of biology to him!

Yesterday, I was just trying to gather a fragment of family for Thanksgiving — my kids are all so dispersed that we need to make a long drive to collect the one, my oldest, who is still living somewhere in the state of Minnesota — when someone popped up to portentiously declare to me (and a gaggle of other science twitter people) that Nature magazine has decreed that biology has no foundation in science. Oh, really?

So I gave the article a quick read. It turns out that no, it hadn’t said that at all, but what it did say was that the consensus of biologists was that a cherished opinion he held was wrong, and since Mr Peter Leslie Morris knows more about biology than biologists, Nature had abandoned all reason and was denying True Biology, his version of biology. I gave him a quick reply, and then charged off to St Cloud to scoop up my wee liddle child for Thanksgiving (except he’s all growed up now and taller than I am, but he’ll still always be my baby).

But now I’m back home. The baby is sleeping in on the couch, and someone is wrong on the internet.

Here’s the article he claims is wrong and denies all biology. My indignant interlocutor is a TERF. It’s a sensible article that, as I said, shows a better understanding of the breadth and depth of biology than some random pompous code-bro on Twitter. Surprising, I know.

According to a draft memo leaked to The New York Times, the US Department of Health and Human Services (HHS) proposes to establish a legal definition of whether someone is male or female based solely and immutably on the genitals they are born with. Genetic testing, it says, could be used to resolve any ambiguity about external appearance. The move would make it easier for institutions receiving federal funds, such as universities and health programmes, to discriminate against people on the basis of their gender identity.

The memo claims that processes for deciding the sex on a birth certificate will be “clear, grounded in science, objective and administrable”.

The proposal — on which HHS officials have refused to comment — is a terrible idea that should be killed off. It has no foundation in science and would undo decades of progress on understanding sex — a classification based on internal and external bodily characteristics — and gender, a social construct related to biological differences but also rooted in culture, societal norms and individual behaviour. Worse, it would undermine efforts to reduce discrimination against transgender people and those who do not fall into the binary categories of male or female.

Yes, exactly. External sexual characteristics, like genitalia, or even genetic characters, like the presence or absence of a Y chromosome, are not adequate proxies for gender. You can’t look inside someone’s pants and determine what’s going on inside their brain, which is a disturbing thought to the dedicated devotees of gender essentialism. What the article is saying is that sex and specifically gender is a heck of a lot more complex than a rigid binary, where all the various traits — biological, psychological, and cultural — do not fall into two tightly concordant categories. Which one would hope that here in the 21st century everyone would recognize as obvious. One thing we’ve learned, though, is that even in our enlightened age there are a huge number of benighted twits who want to deny reality.

I had asked the pretentious bro-grammer whether he’d actually read the article for comprehension, because of the plain English in this bit.

Even more scientifically complex is a mismatch between gender and the sex on a person’s birth certificate. Some evidence suggests that transgender identity has genetic or hormonal roots, but its exact biological correlates are unclear. Whatever the cause, organizations such as the American Academy of Pediatrics advise physicians to treat people according to their preferred gender, regardless of appearance or genetics.

The research and medical community now sees sex as more complex than male and female, and gender as a spectrum that includes transgender people and those who identify as neither male nor female. The US administration’s proposal would ignore that expert consensus.

As you can easily see, the article plainly states that gender is a spectrum, and that there is a mismatch in some cases between the physical attributes we record at birth, and the preferred gender of the individual. Having a penis isn’t an absolute cognitive determinant.

So he tells me he did too read the whole article, and now he wants me to tell him what the absolute cognitive determinant is. Repeatedly.

The whole point of the article is that there is no biological evidence that will make classification possible. The Trump plan is unworkable. There is no objective scientific test that definitively determines what thoughts, attitudes, and preferences are percolating inside someone’s cranium, and yet they want to insist that being a penis-haver or Y-chromosome-haver is the conclusive, ultimate determinant that one is culturally and psychologically male.

That last one is a real give-away. There is something physical that must determine one’s gender, and anything else is a delusion. This understanding of reality would imply that your thoughts are all delusions. How would he prove that he was a man, if penises and Y chromosomes were not sufficient reassurance? Maybe his concept of manhood is the real delusion. The Western cultural ideal of masculinity trembles on the brink of collapse into fantasy if he can’t simply prove that he is a real man by pulling down his pants…if manhood is simply a shared belief in how one should behave and think as a man, a fixed star that everyone with a Y chromosome must follow by some precious inner biological compulsion.

Here is the truth: this is a political attempt to ostracize people they don’t like.

Political attempts to pigeonhole people have nothing to do with science and everything to do with stripping away rights and recognition from those whose identity does not correspond with outdated ideas of sex and gender. It is an easy way for the Trump administration to rally its supporters, many of whom oppose equality for people from sexual and gender minorities. It is unsurprising that it appeared just weeks before the midterm elections.

Of course, there is also no known biological correlate to ideology, therefore it must be a delusion. Republicans don’t really exist, unless perhaps they can show some Satan’s mark somewhere on their body. Maybe we should strip search all Republicans before they’re allowed to vote?

Mr Peter L Morris went back and forth with other people throughout the day while I was blissfully cruising down I94. I guess he was feeling the heat, because he decided to call in reinforcements.

MICHAEL LAIDLAW? Really? TERFiness confirmed. When you think Michael Laidlaw, ideological endocrinologist, is a legitimate source, maybe we do have an objective criterion for a certain range of thoughts.

I’d rather not get deeply into Laidlaw’s crackpot biology, but fortunately, Zinnia Jones has already ripped into that gomer. Just read that. I cannot resist this direct quote from Laidlaw, though: just so much bad biology.

If gender identity is determined only by genes, then we would expect that identical twins would profess having the same gender identity nearly 100 percent of the time. This is not the case. In fact, the largest transexual twin study ever conducted included seventy-four pairs of identical twins. They were studied to determine in how many cases both twins would grow up to identify as transgender. In only twenty-one of the seventy-four pairs (28 percent) did both identical twins identify as transgender. This is consistent with the fact that multiple factors play a role in determining gender identity, including psychological and social factors. This study in fact shows that those factors are more important than any potential genetic contribution. Furthermore, no genetic studies have ever identified a transgender gene or genes.

No one believes that gender identity is determined only by genes. I repeat what the Nature article says:

Some evidence suggests that transgender identity has genetic or hormonal roots, but its exact biological correlates are unclear.

Laidlaw has a cartoon version of genetics in his head, where everything is absolutely Mendelian. Genes are responsive to the environment, so he simply ignores an important contributor to gender. It’s genes or nothing! Meanwhile, any competent geneticists would look at the data he cites, even just the summary he makes, and tell you that it suggest that there may be a heritable component to gender.

Or if you just want the short summary, read that Nature article. It’s accurate and good biology, unlike anything you’ll hear from Michael Laidlaw MD, or Peter L Morris, Microsoft .NET developer.

That’s the Pinwheel of Doom

Oh, what a pretty pinwheel! Until you look at what it illustrates. The height of each bar is the approximate number of hazards to the human concern listed from the impact of climate change. We’re in big trouble because each hazard compounds the others — it’s saying that if one thing doesn’t get you, something else will, and here’s an objective attempt at real risk assessment.

Six different aspects of human systems are shown (health, food, water, infrastructure, economy and security), with their subcategories for which impacts were observed. The heights of the bars indicate the number of hazards implicated in the impacts. Here we analysed ten climate hazards. The complete table of climate hazards and human aspects impacted is available at http://impactsofclimatechange.info.

The authors conclusion could be shorter. They could have just written “We’re fucked.”

Given the vast number of components in coupled human–climate systems, assessing the impacts of climate change on humanity requires analyses that integrate diverse types of information. Contrasting temporal and spatial patterns of climate hazards, compounded with varying vulnerabilities of human systems, suggests that narrow analyses may not completely reflect the impacts of climate change on humanity. Our integrative analysis finds that even under strong mitigation scenarios, there will still be significant human exposure to climate change, particularly in tropical coastal areas; such exposure will be much greater if GHG concentrations continue to rise throughout the twenty-first century and will not differentiate between poor or rich countries. The multitude of climate hazards that could simultaneously impact any given society highlights the diversity of adaptations that will probably be needed and the considerable economic and welfare burden that will be imposed by projected climate change triggered by ongoing GHG emissions. Overall, our analysis shows that ongoing climate change will pose a heightened threat to humanity that will be greatly aggravated if substantial and timely reductions of GHG emissions are not achieved.

Every election from here on out is going to be all about who is going to save my grandchildren from onrushing doom.

Camilo Mora, Daniele Spirandelli, Erik C. Franklin, John Lynham, Michael B. Kantar, Wendy Miles, Charlotte Z. Smith, Kelle Freel, Jade Moy, Leo V. Louis, Evan W. Barba, Keith Bettinger, Abby G. Frazier, John F. Colburn IX, Naota Hanasaki, Ed Hawkins, Yukiko Hirabayashi, Wolfgang Knorr, Christopher M. Little, Kerry Emanuel, Justin Sheffield, Jonathan A. Patz & Cynthia L. Hunter (2018) Broad threat to humanity from cumulative climate hazards intensified by greenhouse gas emissions. Nature Climate Change doi.org/10.1038/s41558-018-0315-6.