Writing synopses of science articles is hard

Really, it’s harder than you think. Individual science papers typically build on a larger body of knowledge and don’t stand alone; it is assumed that the reader has significant amounts of training in the subject at hand so that the authors don’t bother to fill in all the background. When writing a summary of the article for a general audience, one has to provide a lot of context, without simply reiterating the contents of, for instance, a molecular biology textbook and a year’s worth of upper level biology education. And if someone writing a summary of an article lacks that knowledge altogether, the misinterpretations can be disastrously wrong.

Take this article in TechTimes, Massive Genetic Study Reveals 90 Percent Of Earth’s Animals Appeared At The Same Time. The title alone is creationist clickbait, and the author of the story clearly didn’t understand the article at all. She gets it all wrong.

Landmark new research that involves analyzing millions of DNA barcodes has debunked much about what we know today about the evolution of species.

In a massive genetic study, senior research associate at the Program for the Human Environment at Rockefeller University Mark Stoeckle and University of Basel geneticist David Thaler discovered that virtually 90 percent of all animals on Earth appeared at right around the same time.

More specifically, they found out that 9 out of 10 animal species on the planet came to being at the same time as humans did some 100,000 to 200,000 years ago.

No, it didn’t. The paper says nothing of the kind.

The paper is an analysis of DNA barcodes. DNA barcoding is a process that uses a short stretch of mitochondrial DNA to map an individual organism to a species — it’s a technique that lets you look at a sample of a few cells, amplify and sequence a single gene (COI or COX1 are commonly used in animals), and then unambiguously identify the specific species those cells came from. Being able to do this relies on an interesting property of a species: there is limited variance in the barcode sequence within the species, but there has to be greater variance of that sequence from other, even closely related species. In other words, DNA barcodes form tight little clusters of similarity that correlate well with other criteria for defining a species.

That raises questions. You can read the original article, Why should mitochondria define species?, for yourself and see. The question is about why variations within a species should cluster so tightly. Stoeckle and Thaler propose a couple of hypotheses to explain that phenomenon.

Either 1) COI barcode clusters represent species-specific adaptations, OR 2) extant populations have recently passed through diversity-reducing regimes whose consequences for sequence diversity are indistinguishable from clonal bottlenecks.

It’s a meaty paper that goes through the evidence for both of those hypotheses, and I’m wishing I’d seen this paper last semester, when I was teaching evolutionary biology — there is a lot of useful evolutionary thinking going on here. Maybe I can revoke all of my students’ degrees and tell them they have to come back for one last thing? I think we can go through the paper adequately in about a week, so I’m sure they won’t mind.

Their final conclusion, after analyzing millions of barcodes, is fairly straightforward, I think.

The simple hypothesis is that the same explanation offered for the sequence variation found among modern humans applies equally to the modern populations of essentially all other animal species. Namely that the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past 200,000 years.

This is not saying that there was a single instant in the last 200,000 years from which all modern species arose simultaneously. It’s a statement about the process of speciation: species arise from isolation of a limited subset of an existing population, which is why they have limited variation in their DNA barcodes, followed by an expansion of the new species’ population, during which the DNA barcodes accumulate variation slowly.

No, they did not find out “that 9 out of 10 animal species on the planet came to being at the same time as humans did some 100,000 to 200,000 years ago”. New species arise continuously, but they do so by going through a population bottleneck in geologically recent times. Homo sapiens arose as a distinct species between 100,000 and 200,000 years ago, but that notorious London Underground mosquito may have evolved in the 18th century…which is still within the past 200,000 years, you may notice.

It’s a bit like reading a statement that almost all people are less than 100 years old, and then wondering, publicly and in print, about what happened in 1918 to cause every human being on Earth to have been suddenly born in that year. That must have been some orgy to celebrate the end of the Great War.

Flattered, then humbled

Today I read an article that listed a few of the colossal errors of Jordan Peterson, and I was flattered to be cited by the author.

However, using the coincidence of serotonin as the supposed basis for behavioural parallels between lobsters and humans – trumpeted during the Channel 4 interview, again to give off the impression of scientific authority – has been expertly dismantled by the biologist PZ Myers. Evidently irked by Peterson’s intellectual overreaching, Myers claims that Peterson has “built a case on false facts and distortions of general observations from the scientific literature. He has not demonstrated anything about socio-cultural constructions. Not only does he get the evidence wrong, he can’t construct any kind of logical argument…”

Worse still, Myers argues, there is an ideological motive for all this: “Peterson is distorting the evidence to fit an agenda… It’s appalling the degree to which this man is asserting nonsense with such smug confidence. This man is lying to you.”

Oh, “expertly dismantled”…thank you, thank you, I wave to the audience and blush charmingly. I am gratified to be appreciated. But then…Google throws a bucket of ice-cold humility in my face and suggests that I go read this excellent article in the Washington Post by Bailey Steinworth.

Oh, man, it is so good. She points out that “in asking us to consider the lobster, he’s cherry-picking one model of social behavior when there’s a whole ocean full of equally relevant examples”, and then…she gives several examples. It’s beautiful.

As a psychologist, Peterson understandably seems to favor lobsters because of their well-characterized behavioral repertoire, citing among other things research on the neurotransmitter and antidepressant target serotonin. But they’re not the only inhabitant of the ocean that’s been studied in this way. He might also be interested in Aplysia. Like lobsters, sea hares of the genus Aplysia — sea slugs named for sensory structures that resemble rabbit ears — have been used extensively in serotonin studies. Behaviorally, however, lobsters and sea slugs could hardly be more different: While a lobster rarely wants to see another lobster, a sea hare placed on its own will crawl toward chemical cues indicating the presence of other sea hares. In fact, being with other members of its species improves a sea hare’s ability to learn and remember. Peterson’s opening chapter emphasizes that male lobsters compete for the best territory to win access to the most females. By contrast, in sea hare sex, everyone gets a turn. They’re hermaphrodites that mate in groups, alternating between the “male” and “female” roles.

Now that’s an expert dismantling. Go read the whole thing. Of of the dismaying truths of our woefully inadequately educated public, which includes a certain pretentious professor of psychology, is how unaware they may be of the diversity of biological strategies. Nature ain’t respectin’ your Biblical mores, people.

Do not play gotcha games with @upulie, even if you are a billionaire

You all know I’m not a fan of Elon Musk — I think he’s something of a looter, a guy who’s good at PR (usually) and knows what bandwagons to leap upon. But lately he’s been working so hard to confirm all of my biases against him.

He announced a plan to fund a media watchdog site that would rank news sources…which is a fine idea, except that his criteria seemed to be self-serving. A news source that was critical of Elon Musk would be “fake news”, obviously. And then what happens? Musk endorses a propaganda site run by a sex cult.

But what really annoyed me was his ignorance and arrogance when he sneered at Upulia Divisekera because she studies nanotechnology.

So Upulie responded with a whole series of tweets outlining the importance of nanotechnology. But guess what? After his initial snipe, he just ignored her altogether. I think that means that she kicked his ass.

At least a nice summary of the Musk mythos emerged out of that mess.

Good news from our little home on the prairie

Go say hello to Rob Denton — he writes at the group blog, The Molecular Ecologist, and he’s got a very nice post up about species differentiation rates varying with locomotion mode. Basically, terrestrial organisms form more species than aquatic or flying organisms, because they face more geographic barriers.

No, he’s not joining freethoughtblogs. It’s even better: he’s joining the University of Minnesota, Morris biology faculty, so he’s going to be hanging around here in the upper midwest for a while. See? That job search I was part of around Christmas of this year had a successful outcome.

Also, the two job searches I chaired last month also were extremely successful, and we snared a couple of phenomenal colleagues who will also be starting here in the fall…but I’ll say no more until they’re actually here. Boy, this place is going to have a lot of new faces and some big changes this year!

Is the first rule of science communication “Be mealy-mouthed”?

Hot on the heels of The Sun, here comes Newsweek, touting that drivel about cephalopods from space by Steele et al.. I have dispensed enough scorn for that paper lately, so now I’m going to snarl at a few other targets: some of the critics.

Outside experts are unconvinced by the findings. Avi Loeb, the Frank B. Baird Jr. Professor of Science at Harvard University, told Newsweek the paper raised “an interesting but controversial possibility.”

Oh, fuck that noise. That’s the polite reservation of a privileged professor who would rather not offend a peer. It was not “interesting”. There is nothing interesting about the hypothesis. This is antique bullshit biology by a dead astronomer who knew nothing of the subject, and it’s been kicked around for years by his (ma)lingering acolytes. It is not compatible with any of the evidence, and it doesn’t even make sense: it contradicts all the available evidence.

It is also not “controversial”. It is fucking wrong. I know it goes against years of science training, which tells everyone to fudge and hem and haw and avoid saying anything that might someday be used to say you were wrong about something, but get over it. Learn to speak plainly and honestly. This kind of dim politesse is exactly what allows science denialists to misquote you.

However, it offers no “indisputable proof” that the Cambrian explosion is the result of panspermia, he said.

Aaargh. First day of my introductory biology course, where I talk about the basic principles of science, the first thing I tell them is that THERE IS NO PROOF IN SCIENCE. We deal in probabilities, in consilience, in building an evidential case to strongly support a hypothesis, and everything is provisional.

The problem with the squid panspermia hypothesis isn’t that there is no proof, it’s that there is no evidence. None. The dithering pontifications in the paper in question are all evidence-free speculations based on wishful misinterpretations of inappropriately collected and interpreted data.

I bet that Harvard professor would say exactly the same thing over a beer at the local bar with his colleagues, but put ’em in front of a journalist and suddenly all of their well-earned confidence turns into cautious cowardice.

And thus do all the phony hucksters and pseudoscientists thrive in the loamy fertilizer of tepid, timid compost dribbling from the jaws of hesitant academics.

I just had an idea for a movie: SQUIDNADO!

I got email this morning…and so did every member of the science & math division at the University of Minnesota, Morris. This happens every once in a while, since our official email addresses are all publicly accessible, and anyone can grab them and spam the heck out of us all. What was unusual is that this email was directly addressed to me, personally, and the sender decided that he needed to put me in my place and flaunt his erudition to every one of my colleagues.

I am unperturbed by his effort, because in every case, without exception, the loon just ends up exposing his inanity. I mean, you’ve got to realize that trying to harass an entire university division is a poor decision in the first place, right? That thinking that most of the faculty are at all interested in your disagreement with me is somewhat delusional? That you’ve immediately put the wrong foot forward by arbitrarily spamming a whole mob of disinterested people with your long-winded and ultimately pathetic excuses?

You should have known that I’d happily post your email to my blog, where people can opt-in and choose to read the whole thing voluntarily. So yes, I include every word of the thing below.

It’s from Ted Steele, who wrote that very silly article, Cause of Cambrian Explosion – Terrestrial or Cosmic?, in which he proposed that squid fell to earth in comets. I laughed at it in my article, Squids from SPAAAAAAAAACE!, and what has irritated him is that my criticisms were picked up by that prestigious newspaper, The Sun, in an article titled ARE YOU SQUIDDING? Are octopuses aliens? Bizarre new theory suggests the sea creatures’ eggs arrived on earth on a comet from outer space. So the real concern is that a bunch of working class blokes are going to be reading their paper down at the pub, looking for topless pics and anti-immigrant rants, and they’re going to stumble across this weird American egghead who thinks Ted Steele is full of crap.

I think he should be more concerned that The Sun finds his work amusing than that I think it’s garbage. But read on. He’s indignant.

[Read more…]

The Science, Space and Technology Committee is run by dull stupid clowns

You must have heard about the gaggle of stupid Republicans who had a meeting to deny climate change and tell a climate scientist their favorite pet hypotheses to excuse humanity from any responsibility, right? It was reported in Science magazine. These rich twits really did that.

Rep. Dana Rohrabacher (R-CA) said he was bothered that established climate science has not been questioned more by the committee, which has accused federal climate scientists of fraudulently manipulating climate data and subpoenaed their records.

“I’m a little bit disturbed by, No. 1, over and over again, I hear, ‘Don’t ever talk about whether mankind is the main cause of the temperature changing and the climate changing,'” he said. “That’s a little disturbing to hear constantly beaten into our heads in a Science Committee meeting, when basically we should all be open to different points of view.”

Rep. Lamar Smith (R-TX), chairman of the committee, entered into the record an opinion piece published in The Wall Street Journal yesterday that claimed sea levels are not rising because of climate change, a view that rejects thousands of scientific studies. The piece was written by Fred Singer, who is affiliated with the Heartland Institute in Chicago, Illinois, which promotes the rejection of mainstream climate science.

“To solve climate change challenges, we first need to acknowledge the uncertainties that exist,” Smith said in his opening remarks. “Then we can have confidence that innovations and technology will enable us to mitigate any adverse consequences of climate change.”

At one point, Smith showed a slide of two charts that he said demonstrated how the rate of sea-level rise does not equal the sharp spike in the consumption of fossil fuels. When Smith pointed out that rates of sea-level rise have only increased slightly compared with the rate of fossil fuel use, Duffy pointed out that his chart was from a single tide gauge station, near San Francisco, and that sea levels rise at different rates around the world. Smith did not show rising atmospheric CO2 levels or temperatures, both of which have climbed steadily in recent decades as emissions have increased.

The champion, though, was this bozo.

Rep. Mo Brooks (R-AL) questioned Duffy on the factors that contribute to sea-level rise, pointing out that land subsidence plays a role, as well as human activity.

Brooks then said that erosion plays a significant role in sea-level rise, which is not an idea embraced by mainstream climate researchers. He said the California coastline and the White Cliffs of Dover tumble into the sea every year, and that contributes to sea-level rise. He also said that silt washing into the ocean from the world’s major rivers, including the Mississippi, the Amazon and the Nile, is contributing to sea-level rise.

“Every time you have that soil or rock or whatever it is that is deposited into the seas, that forces the sea levels to rise, because now you have less space in those oceans, because the bottom is moving up,” Brooks said.

I’m just going to sit back and let Rebecca channel my rage. She does it so well!

The scouring of Lake Sammamish

Most salmon are bold adventurers. They’re born in freshwater streams and lakes, spend a happy childhood frolicking in those relatively safe waters, and then strike out for the rich, salty waters of the sea where there’s far more food, and also far more predators. Orca and sea lions, to name a few, love to welcome the visitors to their maws.

But there always some who decide to stay at home. These are called kokanee salmon, and they stay in their freshwater homes all of their lives. They tend to be smaller than the relatives who go to sea, and they form their own unique population structures and gradually set themselves apart from others. I’ve always pictured them as the hobbits of the salmonid world, the comfortable homebodies.

There’s a price to pay, though, because their bucolic homes are at risk as humans intrude. Lake Sammamish in Washington state is one of those places where a population of kokanee live. It used to be an idyllic lake, surrounded by forests that sheltered it, but even when I was a kid I heard about the tribulations — the trees were cut down, the lake cabins went up, then the expanding suburbs of Seattle started to encroach. It’s just east of Bellevue and south of Redmond. It became surrounded by parking lots and city streets and office buildings, and the runoff from the regular rains was no longer filtered by the forests, but instead carried a toxic soup of engine oil and lawncare products right into the once-pristine habitat of the kokanee.

And now it’s worse. Five years ago, 18,000 kokanee lived in the lake; now it’s down to…twenty. Not 20,000, just 20. What has killed them?

County biologists are now tasked with studying the unexpected problem to determine what is causing the species to disappear. Parasites, bacteria, and other diseases are suspects. But a likely factor is the increase in high temperatures throughout the year. Recent years have been warmer, with hotter streaks. This warms the water and lowers oxygen levels for the fish.

Now the lesson you might take from this is don’t be a stay-at-home, get out there and explore the world and set broader horizons for yourself. Getting trapped in a single habitat is risky, and all those intrepid wanderers of the salmon world have escaped this peril on the high seas.

I would suggest an alternative interpretation, though. The lakes are warming first, but the oceans are also warming, more slowly and more irreversibly. The anadromous fish have a refuge now, but we humans are coming for them, too, and they’ve only delayed the inevitable. The real lesson is that all populations are vulnerable, that what we think of as a tiny, incremental change, like a few degrees of temperature rise, can lead to catastrophic collapse. They can be resilient and bounce back from some changes, but eventually they can no longer compensate and will fall apart with terrifying swiftness. From 18,000 to 20 within a few years — that’s an apocalypse for one special population of salmon.