Busy busy busy

I’ve been neglectful of everything! But then, I’m in the midst of a sudden surge of work.

First, on Saturday, 9 February, I’ll be speaking via an electronic connection (like someone from the future!) to the Secular Humanists of Western Lake Erie on Charles Darwin and the Web of Interconnectedness, part of their Darwin Day celebration. Here’s the abstract:

Charles Darwin was a conventional naturalist of his day, and yet he had this great insight that led to a revolution in biology. Where did that come from? I will argue that it was from a shift in perspective, from trying to figure out how a species becomes well suited to its environment, to considering the environment wholistically and seeing how many species of plants and animals, as well as geology, interact to generate forces in biology. What made Darwin’s idea great was that it also interacted with a multitude of other ideas to inspire change across whole fields of science. Evolution led to ecology and genetics, and eventually to molecular biology and genomics, none of which would exist without the seed Darwin planted.

I’ll be doing this live at the West Toledo Branch Library, but I’ll probably also turn it into a video later. Right now the talk is a shambles, but I’ve got a couple of days to whip it into shape. Right?

Second, I’ve got a big messy YouTube video in the works, which is also currently a shambles. Yes, my desktop is in a state of chaos, true wreckage with debris scattered all around. This one is kind of complicated and messy — I’m trying to explain how the concept of human genetic immortality, which leads to horrors as diverse as hereditary royalty and racism, is a toxic lie that poisons society. It’s also biological bullshit that annoys me greatly.

Third…I’m planning a summer research project that might — almost certainly — require IRB approval. I’m proposing to survey various sites around Stevens County for their spider populations, including people’s homes (I’m most interested in synanthropic species), and correlating factors in the environment with spider density by taxon. That involves looking at how cluttered garages are, what pesticides are being used, age of residences, etc. I was working out this stuff and realized that I’ll be generating a database that includes people’s addresses (which will be kept private) and the physical state of their homes, and the operative word there is “people”, not just spiders, dang it.

I’ve never had to do this before. But unlike some twits in Portland, or their apologists in Boston or Oxford, this twit in Small Town, Flyover Country thinks maybe he should make sure everything is kosher before he recruits students and charges off to knock on people’s doors.

So I’ve been trying to read the University of Minnesota protocols for a new study. They are somewhat daunting.

It’s sinking in that I’ve got to have a fairly complete and detailed protocol in hand, and then I’ve got to submit a bunch of stuff to the IRB, so I’m trying to put together a comprehensive preliminary survey, listing everything I might want to ask about a site. I don’t think it’ll have any problem sailing through — I won’t be handing out fun experimental drugs, or performing exciting surgeries on anyone — but The Forms Must Be Followed.

That’s my life for the next week or two, I think.

A lifetime of science!

Hey, look — the esteemed scientist who helped shape my education is getting acknowledged for his work. Not the work he struggled with in getting me to finally graduate, but his work on zebrafish. Chuck Kimmel is getting a lifetime achievement award from Oregon Academy of Science.

“Importantly, Chuck saw the virtue of zebrafish as a genetic model for studies of vertebrate development, due to the relative simplicity of its embryonic cell lineage compared to other vertebrates, its optical clarity during embryogenesis and its rapid generation time,” Bowerman wrote. “It is truly remarkable how Chuck’s insight has had such a global impact, with hundreds of laboratories throughout the world now using zebrafish as one of the two leading models for vertebrate development and behavior.”

In case you are wondering, the #1 model is the mouse. Zebrafish are #2, but at least you don’t need to disembowel Minnie Mouse to get access to embryos.

I knew Chuck would do good in his career. Way back in the day we also knew zebrafish would be a popular tool.

The Little Ice Age was anthropogenic?

Climate change denialists love to bring up the Little Ice Age (and the Medieval Warm Period before it) as examples of natural variation in climate that wasn’t human-caused, and therefore cast doubt on all the arguments about anthropogenic climate change. Except…what if the cooling recorded for the 17th-19th centuries was actually caused by human activity? A new analysis suggests that that might be our fault, too.

It’s the UCL group’s estimate that 60 million people were living across the Americas at the end of the 15th Century (about 10% of the world’s total population), and that this was reduced to just five or six million within a hundred years.

The scientists calculated how much land previously cultivated by indigenous civilisations would have fallen into disuse, and what the impact would be if this ground was then repossessed by forest and savannah.

The area is in the order of 56 million hectares, close in size to a modern country like France.

This scale of regrowth is figured to have drawn down sufficient CO₂ that the concentration of the gas in the atmosphere eventually fell by 7-10ppm (that is 7-10 molecules of CO₂ in every one million molecules in the air).

“To put that in the modern context – we basically burn (fossil fuels) and produce about 3ppm per year. So, we’re talking a large amount of carbon that’s being sucked out of the atmosphere,” explained co-author Prof Mark Maslin.

It’s horrifying enough that the American genocide killed about 50 million people, but that it was so immense that it affected the climate is stunning. I also have to wonder how much the earlier Black Death in Europe contributed to a decline in CO2.

This does suggest an obvious solution to our current climate change concerns. Annihilate a few billion people, and the problem goes away.

It looks like the American and Russian leaders are working on a plan to do just that.

Microbiologists don’t need labs, apparently

All they need to do is visit student residences.

A student died after eating leftover pasta that had been left on his kitchen benchtop for five days.

The 20-year-old from the Brussels in Belgium became sick after eating leftover spaghetti with tomato sauce which had been prepared five days earlier and stored at room temperature.

Many thoughts are wheeling through my brain right now.

What kind of environment was this in that food left out for 5 days wasn’t covered in green fur?

Was it all furry with mold, and the student ate it anyway?

I don’t eat food that’s been refrigerated for more than a few days. How desperate was this person? What circumstances led someone to such a dire meal?

I don’t recommend this as an analysis tool, but how did it taste? Shouldn’t the first mouthful have been his first warning?

He became violently ill after eating it. Second warning. You’ve just done something incredibly dangerous.

I wonder how many student kitchens are greater health hazards than anything they might encounter in a microbiology lab. On second thought…I don’t want to know.

Students do not deserve death for poverty and carelessness. How about if we all recognize that what grows on our food and what we stuff in faces might be the greatest threat to our health and survival?

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.