Science needs specific, informed, productive criticism

Professor Dave demolishes Sabine Hossenfelder.

I feel that. The topic of my history class last week and this week is about bias in late 19th/early 20th century evolutionary biology, and how we have to be critical and responsible in our assessment of scientific claims. It’s tough, because I’m strongly pro-science (obviously, I hope?) but I keep talking about dead ends and errors in the growth of a scientific field, and I have to take some time to reassure the students that our only hope to correct these kinds of problems is…science. I also have to explain that the way the errors are discovered is…science, again.

I’m not specifically interested in Sabine Hossenfelder — I don’t watch her videos, not even the ones that might contain good information — but I am concerned with the general problem of how anti-science propaganda manages to advance the causes of dogma. If science gets something wrong, as it does sometimes, it does not mean that superstition or bigotry are right. Raging against the whole of the scientific establishment and the scientific method is how you get RFK Jr put in charge of the NIH. I don’t think that even Hossenfelder believes that will be an improvement.

Can we demand an ethical standard for government?

A common sense act has been introduced in congress, HR 926, asking for basic ethical requirements for the Supreme Court. It sounds like something that ought to be in place.

This bill makes various changes related to the ethical standards, financial disclosure requirements, and recusal requirements that apply to Supreme Court Justices.

Among the changes, the bill requires the Supreme Court to:

adopt a code of conduct for Justices and establish procedures to receive and investigate complaints of judicial misconduct;

adopt rules governing the disclosure of gifts, travel, and income received by the Justices and law clerks that are at least as rigorous as the House and Senate disclosure rules; and

establish procedural rules requiring each party or amicus to disclose any gift, income, or reimbursement provided to Justices.

Additionally, the bill expands the circumstances under which a Justice or judge must be disqualified; and

requires the Supreme Court and the Judicial Conference to establish procedural rules for prohibiting the filing of or striking an amicus brief that would result in the disqualification of a Justice, judge, or magistrate judge.

That’s excellent, and there’s a push to get everyone to call up your state representative to support this bill.

I agree with the bill, BUT…

I have no hope.

The fascists take over the government in January, and they’ll kill this bill. They already have. It was introduced in February of 2023, and it’s gone nowhere. Are we supposed to expect a miracle in the next two months?

I have another problem. If you actually go to the site promoted in that image, the first thing you will see is a plea for donations. It’s all about money. They also ask for your phone number, which I’ll never give out again. I made a donation to the Harris campaign months ago, and they passed my number to other organizations, so I was getting dozens of text messages every goddamned day. They all had a stop code you could send to end the noise, but I discovered that they honored it in name only. The organization I requested to stop would stop, but then they’d pass my number to a different, related organization, and the texts would continue. “Retired Democrats 2024”? “Blue Battleground Project”? “GenBlue PAC”? I didn’t sign up for any of those, and somehow they got my number. I don’t trust Democratic fundraisers.

Maybe we should start by demanding an ethical standard for all political organizations?

I know this is a mixed message. I think putting an ethical standard on the Supreme Court is important, but the Democrats are proving themselves venal and ineffectual.

You have to admire their cunning

Every year, around this time, as the weather gets colder, we get an influx of mice moving into our house to find refuge. Our cat is useless — she makes a lot of noise, usually in the middle of the night, but she can never deliver the coup de grace.

It seems I already have a potential solution at hand.

Warning: the videos below show mice meeting a horrible end in the webs of black widows.

[Read more…]

So that’s how they missed me

The rich have a well-funded network that has been poisoning the collective mind of the country, yet somehow they have failed to penetrate my soft, permeable, liberal skull. How could that be?

“every common hobby for young men–gaming, sports, fitness–is saturated with right-wing propaganda”
Bluesky

There it is, they targeted “gaming, sports, fitness” thereby completely bypassing all of my interests.

Another point not mentioned: have you ever noticed that the biggest, most popular YouTube channels are typically targeted at…children? Mr Beast, PewDiePie, Logan Paul, etc. Then there are lesser channels with a teenaged audience, like Fresh and Fit or Andrew Tate. I’ve skipped over those by getting old. I’m so lucky.

Another step in the evolution of multicellularity

I’m not a fan of phys.org — they summarize interesting articles, but it’s too often clear that their writers don’t have a particularly deep understanding of biology. I wonder sometimes if they’re just as bad with physics articles, and I just don’t notice because I’m not a physicist.

Anyway, here’s a summary that raised my hackles.

Chromosphaera perkinsii is a single-celled species discovered in 2017 in marine sediments around Hawaii. The first signs of its presence on Earth have been dated at over a billion years, well before the appearance of the first animals.

A team from the University of Geneva (UNIGE) has observed that this species forms multicellular structures that bear striking similarities to animal embryos. These observations suggest that the genetic programs responsible for embryonic development were already present before the emergence of animal life, or that C. perkinsii evolved independently to develop similar processes. In other words, nature would therefore have possessed the genetic tools to “create eggs” long before it “invented chickens.”

First two words annoyed me: Chromosphaera perkinsii ought to be italicized. Are they incapable of basic typographical formatting? But that’s a minor issue. More annoying is the naive claim that a specific species discovered in 2017 has been around for a billion years. Nope. They later mention that it might have “evolved independently to develop similar processes”, which seems more likely to me, given that they don’t provide any evidence that the pattern of cell division is primitive. It’s still an interesting study, though, you’re just far better off reading the original source than the dumbed down version on phys.org.

All animals develop from a single-celled zygote into a complex multicellular organism through a series of precisely orchestrated processes. Despite the remarkable conservation of early embryogenesis across animals, the evolutionary origins of how and when this process first emerged remain elusive. Here, by combining time-resolved imaging and transcriptomic profiling, we show that single cells of the ichthyosporean Chromosphaera perkinsii—a close relative that diverged from animals about 1 billion years ago—undergo symmetry breaking and develop through cleavage divisions to produce a prolonged multicellular colony with distinct co-existing cell types. Our findings about the autonomous and palintomic developmental program of C. perkinsii hint that such multicellular development either is much older than previously thought or evolved convergently in ichthyosporeans.

Much better. The key points are:

  • C. perkinsii is a member of a lineage that diverged from the line that led to animals about a billion years ago. It’s ancient, but it exhibits certain patterns of cell division that resemble those of modern animals.
  • Symmetry breaking is a simple but essential precursor to the formation of different cell types. The alternative is equipotential cell division, one that produces two identical cells with equivalent cellular destinies. Making the two daughter cells different from each other other opens the door to greater specialization.
  • Palintomic division is another element of that specialization. Many single-celled organisms split in two, and each individual begins independent growth. Palintomic division involves the parent cell undergoing a series of divisions without increasing the total cell volume. They divide to produce a pool of much smaller cells. This is the pattern we see in animal (and plant!) blastulas: big cell dividing multiple times to make a pile of small cells that can differentiate into different tissues.
  • Autonomy is also a big deal. They looked at transcriptional activity to see that daughter cells had different patterns of gene activity — some cells adopt an immobile, proliferative state, while others develop flagella and are mobile. This is a step beyond forming a simply colonial organism, is a step on the path to true multicellularity.

Cool. The idea is that this organism suggests that single-celled organisms could have acquired a toolkit to enable the evolution of multicellularity long before their descendants became multicellular.

I have a few reservations. C. perkinsii hasn’t been sitting still — it’s had a billion years to evolve these characteristics. We don’t know if they’re ancestral or not. We don’t get any detailed breakdown of molecular homologies in this paper, so we also don’t know if the mechanisms driving the patterns are shared.

I was also struck by this illustration of the palintomic divisions the organism goes through.

a, Plasma membrane-stained (PM) live colonies at distinct cell stages, highlighting the patterned cleavage divisions, tetrahedral four-cell stage and formation of spatially organized multicellular colonies (Supplementary Video 5). b, Actin- (magenta) and DNA-stained (blue) colonies at distinct cell stages showcasing nuclear cortical positioning, asymmetrical cell division (in volume and in time) and the formation of a multicellular colony. This result has been reproduced at least three independent times.

Hang on there : that’s familiar. D’Arcy Wentworth Thompson wrote about the passive formation of cell-like cleavage patterns in simple substrates, like oil drops and soap bubbles, in his book On Growth and Form, over a century ago. You might notice that these non-biological things create patterns just like C. perkinsii.

Aggregations of oil-drops. (After Roux.) Figs. 4–6 represent successive changes in a single system.

Aggregations of four soap-bubbles, to shew various arrangements of the intermediate partition and polar furrows.

An “artificial tissue,” formed by coloured drops of sodium chloride solution diffusing in a less dense solution of the same salt.

That does not undermine the paper’s point, though. Multicellularity evolved from natural processes that long preceded the appearance of animals. No miracles required!

A theological dilemma

A silly speculation: what if you die, go to heaven, and discover that a god had a set of fundamental rules that it didn’t tell anyone about?

I was initially sympathetic to the idea that a god would judge you for doing harm to small helpless creatures — I avoid killing insects without cause — but then there were a few disparaging comments about spiders, natural given the god’s nature, and I started tallying up my invertebrate body count, and I realized that the video character’s tally of having killed 11,000 insects was pathetic.

I’d be going to bug hell, wouldn’t I?

My unpleasant Christmas memory

I’m in the mood for some self-abasement, and also to nod in the general direction of the Xmas season. I’m going to tell you about the most horrible, embarrassing moment of my life so far. Maybe it’ll inspire you to mention your moment of humiliation in the comments to make me feel a little better.

In my youth, I was a regular church-goin’ kid. Sunday school every week, choir every Wednesday, confirmation every Thursday. I was not a believer, but it was the only club that would accept me, and I also liked the music–I was attending more for the choir than anything else. I had a few friends in the group, although…we weren’t good friends, I guess. We never socialized outside the church.

One year we were organizing for a giant Christmas concert involving dozens of churches in the Puget Sound area. We had to do multiple practices every week, and it wasn’t just walking down the street to my local Lutheran church. We were rotating among various churches, a different one every time, to practice together. It was a huge effort, my parents were ferrying me all over the region for a few months ahead of time. I didn’t mind. I had zero patience for the religious nonsense, but if you’ve ever been in a choir, you know that the feeling of singing in harmony with a large group is an almost primeval, inspiring sensation.

The day of the Christmas concert, we loaded up in vans and busses and journeyed to the site of the event: the Kingdome. I told you it was big. The stadium was filled up. All the Washington state choirs were seated in a vast array in the center. When we started singing, we made the whole place vibrate.

Unfortunately, I wasn’t feeling my best. In the hours we were there, I started feeling a little woozy. Then I was trembling. Then I had a cold sweat. Was I nervous? Not really. It’s not as if I had a solo, I was one among many hundreds.

Then it was time for my church group to sing their special song. We stood up, and we started singing the song we’d practiced so hard: “O Come O Come Emmanuel and ransom captive Israel That mourns in lonely exile here,
Until the Son of God appear.” Maybe you know it; I still remember the lyrics because damn, we repeatedly sang that thing so many times before the concert. I stood with my church group, raising my voice before the entire Kingdome audience with cameras aimed at us to record the event.

“O COME O COME…” I sang, wobbling and sweating, and then, suddenly, I felt Satan rising up in my body, like a greasy bubble of demonic filth, then “EMMANUE…” and it hit me, unexpectedly and irresistible, and I started vomiting. Projectile vomiting. A horrific geyser of godliness was instantly purged from my body in an terrible public display.

I did immediately feel better, with one regret: the girl in the row in front of me had a lovely cashmere sweater folded over the back of her chair, and I destroyed it. Sorry.

Our choir director, Mrs Whalen, was incredibly nice and gracious, given that all anyone was going to remember of our hard work and our performance was the kid in the middle who grossed out the entire Kingdome with his horrifying expulsion of bodily fluids. She was one of my favorite people, and she treated my ghastly spectacle with nothing but kindness. I continued on with the choir for maybe a year afterwards, before my inability to reconcile my complete lack of faith and aggressive skepticism with the whole goofy church scene drove me away.

That memory still comes back occasionally these many years later, usually around the holiday season, and I can never hear that hymn without being triggered. I also don’t sing anymore.

So what psychic scars do you all still carry?

Witness them

There is a group of people who monitor deportation flights out of Boeing Field, and other airports.

Heroes witness fascists

The observation room at Boeing Field offers what is arguably America’s best real-time window into our vast network of privately run deportation flights, a system that has generated troubling reports of passenger mistreatment and in-flight emergencies.
…
While news organizations have reported on some of these incidents aboard what the government calls ICE Air, key details about how the system works would still be hidden were it not for a group of researchers who are now part of the work inside the observation room.

The people and organizations behind these flights have been playing dumb for years — they don’t want to talk about them. They drive busses loaded with people right up to the boarding stairs for these planes; they position jailers and vehicles to obscure any view of the people being herded into the planes. They don’t want us to know about them.

The Washington human rights center’s investigation of ICE Air began in 2018 with a modest goal: to prove that deportation operations took place at King County International Airport, as Boeing Field is officially known. Liberal local officials had enacted various “sanctuary” policies to insulate their residents from then-President Donald Trump’s crackdown on immigrants, but they were unaware (or could at least claim to be unaware) of ICE flights at the county-owned airport. “They all played dumb,” said Maru Mora Villalpando of the immigrant rights group La Resistencia. “All of them were like, ‘Wait, what, there are deportations happening here?’”

Yes, we know they are, thanks to dedicated defenders of civil liberties who try to monitor these flights.

The center began gathering documents that proved it, and also hinted at the worldwide breadth of ICE Air’s network. Their investigation grew. Through records requests to ICE, and after interventions by Washington’s congressional delegation, researchers obtained an ICE Air database spanning eight years of global operations: 1.73 million passenger records from nearly 15,000 flights to and from 88 U.S. airports — Boeing Field indeed among them — and to 134 international airports in 119 countries around the world.

Those dang liberals in Western Washington state began shutting off support to these flights, and ICE began getting even more secretive about them.

A game of cat and mouse had begun, pitting the Trump administration — and later the Biden administration — against local sanctuary advocates.

First, ICE switched locations. It began charter operations out of a municipal airport in the small city of Yakima, located in the farming region about three hours east of Seattle.

But activists began showing up at the Yakima airfield, recording tail numbers and keeping count of people being deported.

Second, ICE changed its flight numbering system. The human rights center had disclosed in its 2019 report that it used the federally assigned prefix “RPN-” for “repatriate” to plug information into free flight-tracking websites and obtain a plane’s tail number and ownership. So ICE dropped the “RPN-” and adopted the call signs of its various charter companies.

Wait a minute…if these flights are perfectly legal, why is ICE trying to hide them?

I repeat: WHY ANY SECRECY AT ALL?

And why does ICE only release strongly edited, even blurred, images of detainees on flights? It’s almost as if they think we might see some brutality.

The 97 videos ProPublica examined, ranging in length from 22 seconds to almost 3 minutes, show signs of careful framing and editing. While detainees are commonly shown climbing the steps in handcuffs and the waist chains that secure them, the videos often cut to a new shot before leg shackles can make an appearance. When leg shackles are visible, they are typically out of focus, discernible only if you know to look for them.

It is common on ICE Air to place passengers in five-point restraints — wrists, ankles, and waists in chains — even as the agency’s own statistics show that less than half of the people deported in 2023 had any kind of criminal conviction, let alone for serious felonies that could suggest a possible risk to others on board.

What ICE’s online videos don’t show is revealing in its own right. In spring 2023, the center obtained a series of ICE Air incident reports detailing various accidents during charter operations, including the one in which a detainee in Alexandria, Louisiana, tumbled down the boarding stairs. Agency investigators recommended that contractors and subcontractors avoid such accidents in the future by placing a guard midway up the stairs to help detainees board and to catch any who lose their balance.

You will not be surprised that ICE has not bothered to place those guards, thanks to the diligent work of outside observers, documenting everything despite the best efforts of ICE to conceal them.

The flights continue. They will increase in numbers, if Republicans get their way.

But, you say, I am a native born American. I’m not at risk of deportation. Consider this: “A relatively overlooked set of companies whose shares have also seen stellar surges are the controversial American private prison firms. “

The immediate reading of the prison stock rally is that the Republicans have positioned themselves as ‘tough on crime’ – though former President Bill Clinton did much to bring the Democratic party to the game as well – meaning that the number of incarcerated persons under the Trump administration is likely to increase.

There are already about 1.9 million people in American prisons – about 0.5% of the U.S. population, estimated at 345 million in 2024 – per the data from the Prison Policy Initiative.

It is worth pointing out that the figure is comparable to incarceration rates in the USSR at the height of the infamous GULAG System. Adam Gopnik even wrote in 2012 that the U.S. has more people under ‘correctional supervision’ than the Soviet Union ever did.

(By the way, screw Bill Clinton, too.)

I think a clear sign of an expanding fascist state is the police hiding their activities, as well as an eager industry looking forward to building even more prisons.

If it’s not one thing, it’s another

It was hard to get motivated this morning — Fridays are typically low attendance days in the classroom, and I had worked hard to get today’s topic condensed down into a lot of digestible information (we’re talking about the rediscovery of Mendel, the biometrician and Mendelians arguing with each other). I had a presentation that was pretty tight and I thought would help make the conflict comprehensible to a group of liberal arts majors, none of whom are biology majors.

So I get to class today, and was pleasantly surprised to see that I had 80% attendance, which is kind of a miracle. I tell you, standing at the front of a classroom with only 3 students who don’t really appreciate the work you put in to the class is mighty depressing. So I was temporarily heartened that maybe this lecture wouldn’t go to waste, I fired up my laptop and the projector and got ready to tell this exciting story…and the projector is glitched out. It’s not connecting to anything, and is showing me a message that the projector and microphones were not receiving any data since 5:21pm yesterday. Isn’t technology nice that it has become so sophisticated that it can tell you precisely when it broke down?

I fumbled with it for about 15 minutes — that was the show today, watching the old geezer prof toggling switches and poking at a keyboard in front of the class, and seeing everything fail. I ended up giving up, giving them a brief oral summary of the history of biology from 1900-1915, telling them I’ll give them all the details on Monday, and sending them home early. So many smiles from the students! I didn’t tell them that I don’t find that encouraging at all.

Now I’m sitting in an empty classroom waiting for the IT people to show up. At least I can cheer myself up by thinking, hey, this isn’t the worst thing to happen this week.