Beyoncé enchants me again

I’m not at all a fan of country-western music, even though my parents preferred it all the time. They played the classics, though — Hank Williams, Dolly Parton, Johnny Cash, Tammy Wynette, etc. — and I could appreciate that there’s some really good stuff in the genre. It’s just that every time I’d try to listen to it, there’d be some twangy shit about pickup trucks and jingo and utterly unoriginal noise that would drive me away. I never want to hear Lee Greenwood or his ilk ever again.

But then I’d heard that Beyoncé’s country album, Cowboy Carter, is supposed to be pretty good. So I put it on this morning.

I’m blown away. It’s genre-busting but incredibly original and creative, and challenging but enjoyable to listen to. I think I’m going to have to play it again.

If more country music sounded like this, I might be able to suppress my urge to turn off the radio when it comes on.

What are all these plastics doing to us?

In my eco devo course, we’ve been looking at increasingly subtle effects. We started out the semester examining obviously devastating agents in the environment — think thalidomide, stuff that outright kills embryos or causes gross distortions of developmental processes. Then we spent a few weeks looking at endocrine disruptors, agents that perturb developmental signaling and produce embryos with, for example, fertility problems or changes in sexual differentiation. There are a lot of ways chemistry can screw you up short of wrecking external morphology!

This past week we also looked at micro- and nanoplastics, which I personally find have the potential to be a colossal nightmare. The US is producing about 75 million tons of plastic waste each year, and that crap doesn’t go away. You can throw it in a landfill or dump it in the ocean, but it is just physically eroded down into smaller and smaller fragments, allowing it to infiltrate ever deeper into us and our world. Did you know that archaeologists are finding microplastics drifting down into soils 7 meters down, and that they’re finding them in thousand year old sites? We are filling the world with these novel stable polymers, and we have a poor idea of what they’re doing to us.

So we read a paper by Pederson et al. (2020) about the effect of nanoplastics on zebrafish embryos. Like every paper on this kind of topic, it has to tell us about the magnitude of the problem.

Plastic pollution is ubiquitous and an emerging concern in both freshwater and marine environments. Since mass production began in the 1940s, plastic manufacturing has increased rapidly, with 348 million tons produced globally in 2018. Large amounts end up in the oceans, which are now predicted to contain more than five trillion individual pieces of plastic materials (equaling 250,000 tons) in the first 20 m of the water column. Plastics have been identified virtually everywhere: from arctic sea ice to ocean sediments. In freshwater systems, plastics have been identified in large quantities in lakes, rivers, and basins, especially in areas near dense human populations. Their ubiquity has allowed for potential human exposure to plastics through the consumption of aquatic organisms and via drinking water, especially due to the inability of drinking water facilities to entirely remove anthropogenic particles sourced through freshwater environments. In 2019, the World Health Organization (WHO) called for a greater assessment of plastics in the environment after 90% of bottled water was found to contain small plastic particles (World Health Organization). In addition, anthropogenic particles, many of which are likely plastic fragments and fibers, have been detected in over 81% of tap water sources, allowing for an average of 5800 particles to be ingested annually per person.

This paper isn’t even talking about familiar microplastics — it’s all about nanoplastics, particles less than 1µm in diameter. Eventually, all plastics will be broken down to that degree, but we give these an additional boost by intentionally synthesizing these for use in toothpastes and cosmetics and cleansers, and we’ve added <1 parts per billion (ppb) to tens of thousands of ppb to freshwater and marine ecosystems. We don’t have a practical way to remove this stuff. Go ahead, take a swig of that water bottled in plastic, you’ll just absorb those exotic polymers, they’ll be circulating in your bloodstream and getting incorporated into your tissues. You’ll hardly notice.

Zebrafish embryos and larvae swimming in a solution of up to 10000 ppb nanoplastics didn’t seem to mind. There was no effect on mortality, no change in growth rate, no apparent deformities at all. Maybe we’ll all be OK after all.

Except…they do visibly accumulate the plastics in their tissues (they used plastics that fluoresce in the UV).

And then they looked at gene expression in various known pathways — metabolic genes, genes involved in nervous system function, the cardiovascular system — and whoa, they’re just shifted all over the place. It’s a sign of how robust development is that the organism was looking so normal to human eyes. We are all loaded with compensatory developmental mechanisms to make our construction more reliable, and it always impresses me how much damage and insult an embryo can take and still emerge fairly recognizable.

Heatmap indicating predicted upregulation or downregulation in subpathways based on z-scores. (Red is upregulated, blue is downregulated)

One disappointment in the paper is that the behavioral assays were fairly crude, but that’s not the investigators’ fault. They’re working with 5-day old larvae, which, while zebrafish are remarkable little sensory processing machines at that age, they’re still kind of stupid, with a limited behavioral repertoire. The authors looked at spontaneous motor activity, and the fish exhibited a dose-dependent increase in burst swimming. They’re twitchier. More hyperactive. Their brains are being randomly modified chemically, and we’re seeing changes that I’d expect to be more apparent with more sensitive assays.

The message I’m trying to get across to the students is that there is a wide range of phenomena that environmental factors are causing, and we don’t know most of them. It took us decades to get corporations to remove lead from our gasoline, despite the obvious ways it was perturbing our growth and behavior. Are plastics going to be the leaded gasoline of the 21st century?

There is a solution: make biodegradable plastics, ones that don’t reduce to dead stable particles, but instead are digestible by organisms and can be metabolized. Progress is being made in that direction!

An attractive solution to mitigate the environmental impact of microplastics is to develop plastics that do not generate persistent microplastics as part of their normal life cycle. Even plastics that are properly collected and recycled generate microplastics as part of the normal wear from everyday use or as a consequence of recycling or washing processes. Thus, to prevent the accumulation of microplastics, new plastic materials must be developed that are completely biodegradable so that any particles generated from these products will quickly degrade in the environment. Biodegradation is the process by which microbes break down polymers into simpler molecules that can be used as a source of carbon to produce biomass. This requires that the polymer contains chemical bonds, most notably in the polymer’s primary backbone structure, that are physically accessible to enzymes that naturally recognize these bonds as substrates, and that the underlying monomer molecules that are released through this enzymatic cleavage can be consumed by microorganisms. In natural environments, this process is typically performed by consortia of microbes, including bacteria and fungi, secreting hydrolytic enzymes, which sever the polymer to release a variety of monomers and oligomers that can then be utilized as a carbon nutrient source by the microbes. Catabolism of these polymer-derived oligomers and monomers leads to the generation of organismal biomass and CO2 via respiration.

Why would we want structural materials that inevitably break down? Well, maybe you don’t, but I think if we whisper “planned obsolescence” into the ears of corporate executives, maybe they’ll force us to accept them.

Pedersen AF, Meyer DN, Petriv A-MV, Soto AL, Shields JN, Akemann C, Baker BB, Tsou W-L,
Zhang Y, Baker TR (2020) Nanoplastics impact the zebrafish (Danio rerio) transcriptome: Associated developmental and neurobehavioral consequences. Environmental Pollution

A plea for sympathy

When did a dog or cat do so much for you?

I am, of course, giving our cat some side-eye right now.

The cat was looking over my shoulder and reading this as I posted it. Now she’s jumped on my lap, keeping me from my work and forcing me to type one-handed.

I’ve got to be more careful about letting her read the internet.

Boeing has become an object lesson in bad business

Boeing 737 MAXs parked at Moses Lake

It’s time for another depressing story about Boeing, and by extension, a lot of other American institutions that are being wrecked by the capitalist mindset. The situation at Boeing has been going downhill for years.

But Swampy [the nickname for John Barnett, a whistleblower] was mired in an institution that was in a perpetual state of unlearning all the lessons it had absorbed over a 90-year ascent to the pinnacle of global manufacturing. Like most neoliberal institutions, Boeing had come under the spell of a seductive new theory of “knowledge” that essentially reduced the whole concept to a combination of intellectual property, trade secrets, and data, discarding “thought” and “understanding” and “complex reasoning” possessed by a skilled and experienced workforce as essentially not worth the increased health care costs. CEO Jim McNerney, who joined Boeing in 2005, had last helmed 3M, where management as he saw it had “overvalued experience and undervalued leadership” before he purged the veterans into early retirement.

I’m seeing the same thing in the university system: we’ve got MBAs telling us that the universities should discard “thought” and “understanding” and “complex reasoning” and become vocational schools that churn out degrees. The scary twist is that now the same incompetents who got us in this mess are not blaming their own stupid goal-directed approach — the new scapegoat is “DEI,” which is actually beneficial and enables the kind of new perspective that might help us out.

But Boeing is screwed. It’s run by idiots who tout “leadership” but don’t know how to do the job of an aircraft manufacturer. How can you overvalue experience?

“Prince Jim”—as some long-timers used to call him—repeatedly invoked a slur for longtime engineers and skilled machinists in the obligatory vanity “leadership” book he co-wrote. Those who cared too much about the integrity of the planes and not enough about the stock price were “phenomenally talented assholes,” and he encouraged his deputies to ostracize them into leaving the company. He initially refused to let nearly any of these talented assholes work on the 787 Dreamliner, instead outsourcing the vast majority of the development and engineering design of the brand-new, revolutionary wide-body jet to suppliers, many of which lacked engineering departments. The plan would save money while busting unions, a win-win, he promised investors. Instead, McNerney’s plan burned some $50 billion in excess of its budget and went three and a half years behind schedule.

The focus on stock price, as if it’s a meaningful metric of the value of a company (a metric further eroded by stock buybacks) has not been a win-win. It’s been a disaster. They are currently losing tens of millions of dollars on each 787 they build, and their reputation is so bad they’re unsellable.

There’s a terrifying visual representation of this: the satellite view of the Moses Lake Municipal Airport in an arid stretch of Washington east of Seattle, or the Southern California Logistics Airport in Victorville, California, where hundreds of Boeing 737 MAXes sit in abandoned parking lots waiting for someone to fix them so they can finally be delivered. Meanwhile, pieces are flying off the Boeing planes actually in use at an alarming rate, criminal investigations are under way, and another in a long line of stock-conscious CEOs is stepping down. Boeing’s largest union, the Machinists, is trying to snag a board seat because, in the words of its local president, “we have to save this company from itself.”

The company is doomed, because the moneyed assholes have a deathgrip on “leadership.”

SPEEA [Society of Professional Engineering Employees in Aerospace ] has demanded, understandably, that the board choose an aerospace engineer as its next CEO. But there are few signs that will happen: None of the names floated thus far for the spot have been aerospace engineers, and the shoo-in for the position, GE’s Larry Culp, is not an engineer at all.

You might be wondering what kinds of penalties Jim McNerney suffered as a consequence of his catastrophic performance. Why, none at all, of course.

In 2007, as CEO of Boeing, W. James McNerney Jr. made $12,904,478 in total compensation, which included a base salary of $1,800,077, a cash bonus of $4,266,500, options granted of $5,871,650, and Other $966,251.

In 2008, his total compensation increased to $14,765,410, which included a base salary of $1,915,288, a cash bonus of $6,089,625, and options granted of $5,914,440.

In 2009, his total compensation decreased to $13,705,435, which included a base salary of $1,930,000, a cash bonus of $4,500,300, stock options granted of $3,136,251, stock granted of $3,136,242, and other compensation totaling $1,002,642.

In 2013, McNerney made $23.2 million in total compensation, which included a $1.9 million salary, $3.7 million stock award, $3.7 million stock option grant, and an annual incentive bonus of $12.8 million.

In 2014, as Chairman and CEO of Boeing, McNerney made $29 million in total compensation. Of the total: $2,004,231 was received as a salary; $14,400,000 was received as an annual bonus and a three-year performance bonus; $6,272,517 was awarded as stock (none was received in stock options); and other compensation totaling $760,000.

Meanwhile, John Barnett, the whistleblower and competent engineer, is dead. Something is wrong here.

Today is the day of the dog-and-pony show

This may be a terrible mistake. We’ve got a couple of groups of prospective students coming to the university this morning, and they’re going to get guided around the science facilities and their questions answered. We hope to encourage them to enroll here next year. And who was tapped to lead them around?

Only the homeliest, least charismatic, oldest professor in the department, the guy with the lab full of spiders, me. I’m going to have to have a talk with the marketing department.

It’s my own fault. A call went out for volunteers, I happened to have an open time slot at that time, unlike my colleagues who apparently also work harder than I do, so I raised my hand tentatively and got thrown into the machine. I will try to be enthusiastic and informative, but I can only push the raw material so far.

I’m planning to put some of the spiders from the colony under the microscope and project a live video view of them feeding. Do you think that will make our enrollments surge?

How’s your sperm count doin’, guys?

Humans are going to go extinct, says the BBC. “Spermageddon!”, says the Daily Mail. Mankind, specifically, faces doom. If it’s not for disappearing Y chromosomes, it’s our plummeting sperm counts. I don’t know, can women do it all alone?

I had to dig through all this garbage last weekend, as I was preparing to spend another week plowing through the endocrine disruption literature, and considering the effects of things like BPA and pesticides on male developmental biology. In particular, the average sperm count has been declining for the past 50 years. The newspapers were all revved up a while ago over this one paper by Levine et al. (2017), “Temporal trends in sperm count: a systematic review and meta-regression analysis”. It really was one paper that triggered it all, despite all the other papers on the subject, because the author was fond of saying things like, “Eventually we may have a problem, and with reproduction in general, and it may be the extinction of the human species.” It is a serious concern, but hyperbole doesn’t help.

Part of the problem was that all of the secondary sources were using the same or similar over-simplified graph from the paper. This one:

(a) Meta-regression model for mean sperm concentration by fertility and geographic groups, adjusted for potential confounders. (b) Meta-regression model for mean total sperm count by fertility and geographic groups, adjusted for potential confounders. Meta-regression model weighted by sperm concentration (SC) SE, adjusted for fertility group, time × fertility group interaction, geographic group, time × geographic group interaction, age, abstinence time, semen collection method reported, counting method reported, having more than one sample per men, indicators for study selection of population and exclusion criteria (some vasectomy candidates, some semen donor candidates, exclusion of men with chronic diseases, exclusion by other reasons not related to fertility, selection by occupation not related to fertility), whether year of collection was estimated, whether arithmetic mean of SC was estimated, whether SE of SC was estimated and indicator variable to denote studies with more than one estimate. Total sperm count (TSC) meta-regression models weighted by TSC SE, adjusted for similar covariates and method used to assess semen volume.

It’s terrible. Here we have a single parameter, sperm count, that can be easily modified by a host of variables: subject age, whether they smoke, time of last ejaculate, disease state, etc., etc., all in many different observations with different protocols, and they’ve crunched it all down to a straight line. I did not believe it. Where are the error bars, for Onan’s sake?

It’s particularly annoying, because when I worked my way back to the original paper, it included this better figure:

(a) Mean sperm concentration by year of sample collection in 244 estimates collected in 1973–2011 and simple linear regression. (b) Mean total sperm count by year of sample collection in 244 estimates collected in 1973–2011 and simple linear regression.

You could make the valid point that this version is more complicated and doesn’t include all the corrections and adjustments made in the first one, but I’d argue that this one is stripped of the biases of the authors’ interpretations. It still makes the point that sperm counts are going down, but now I can see how noisy the data are.

I also went looking for other articles that assessed the phenomenon, too. For instance, here’s a different 2017 meta-analysis by Sengupta et al. that does a better job of visualizing the data. This, for example, is a bubble plot that illustrates the sample size of each of the constituent data sets.

Temporal decline in sperm concentration (×106/ml) from 1965 to 2015, bubble size corresponds to the number of men in the study.

Look at all that variation! You can see that the earlier studies had much smaller sample sizes, and that the studies ballooned in recent years. If you like more conventional statistical analyses, here’s a box & whisker plot.

Box and whisker plot of sperm concentration data of European men of the past 50 years.

That doesn’t lend itself as well to hysterical over-interpretation, of course. That says instead that we should be carefully studying this real problem, rather than freaking out over the imminent extinction of the human species, which isn’t really happening. There’s so much variation in these numbers that we can console ourselves with the fact that even if we personally are functionally sterilized by the chemical bath we’re living in, there are plenty of men still pumping out lots of sperm to step in and fertilize womankind (which is really a terrible perspective on it all.) One paper I read found that rural men were more strongly affected, but that the men of New York Citaay maintained a robust sperm count. That urban men will do the job of maintaining humanity’s numbers is probably not reassuring to readers of the Daily Mail, though.

The point here is not to diminish the reality of the problem — BPA, atrazine, various pesticides, and fracking chemicals are all doing unpleasant things to our masculine (and feminine!) bits, and we should do something about it. We are being poisoned, it’s just not going to drive us to extinction in the near future. Eventually, yes.

Hagai Levine, Niels Jørgensen, Anderson Martino-Andrade, Jaime Mendiola, Dan Weksler-Derri, Irina Mindlis, Rachel Pinotti, Shanna H. Swan (2017) Temporal trends in sperm count: a systematic review and meta-regression analysis. Human Reproduction Update, pp. 1–14, 2017.

P Sengupta, E Borges, Jr, S Dutta, E Krajewska-Kulak (2017) Decline in sperm count in European men during the past 50 years. Human & Experimental Toxicology,

Buh-bye, Sam

Sam Bankman-Fried was sentenced today to a 25 year prison sentence, which is probably fair since it was less than what I would have vindictively handed down (I am not a judge), but seems fairly substantial.

His comments were mildly amusing.

Given a chance to speak, Bankman-Fried stood and apologized in a rambling statement, saying: A lot of people feel really let down. And they were very let down. And I’m sorry about that. I’m sorry about what happened at every stage.

He added that, My useful life is probably over. It’s been over for a while now, from before my arrest.

What makes you think you ever had a “useful life,” you thieving parasite?

Now we need to lock up all the crypto bros.

I detested the NY Times since before it was cool

Among my earliest complaints was about their editor, Jodi Wilgoren (now Rudoren), who was always waffling over ‘both sides’ in the creation/evolution debate. Those complaints are so old, back 20 years and more, that they were posted when this blog was just a little personal endeavor posted on an old Macintosh in my lab, and you can’t get to them anymore. Wilgoren infuriated me with comments like this one, after she’d dedicated a huge amount of time ‘reporting’ creationist claims about the Grand Canyon.

I don’t consider myself a creationist. I don’t have any interest in sharing my personal views on how the canyon was carved, mostly because I’ve spent almost no time pondering my personal views — it takes all my energy as a reporter and writer to understand and explain my subjects’ views fairly and thoroughly.

So what was she doing writing science articles for the NYT, if she’d never thought about the science?

Anyway, I was reminded of that by this recent comic.

This has always been the way of the NYT. All through the Bush years, the Iraq War, every political issue, the New York Times always been the banner carrier for the passive voice and both-siderism. It’s just the worst.

Wilgoren/Rudoren is now the editor of The Forward, where she has won awards from, among others, the Religious News Association, which is no surprise. It is not clear if she has yet started thinking.

I join the non-engineers in solving engineering problems!

There was a terrible accident at a bridge in Baltimore — it was struck by a container ship and collapsed horrifically. I didn’t think I had anything to contribute to the discussion. Minnesota had a terrible bridge collapse back in 2007, but that was a consequence of neglect and failure to maintain critical infrastructure. This event seems to be completely different.

But then I looked at the news and noticed that a lot of idiots are throwing out explanations. Hey, I have no engineering expertise, know nothing about bridge construction, but have ridden on a ship a few times, therefore I’m just as qualified as the Fox News team or Victor Davis Hansen, or some guy who has appeared on Ancient Aliens, therefore I should opine.

You should look at how they’re explaining the crash.

A non-exhaustive list of things that are getting blamed for the bridge collapse on Telegram and X include: President Joe Biden, Hamas, ISIS, P Diddy, Nickelodeon, India, former President Barack Obama, Islam, aliens, Sri Lanka, the World Economic Forum, the United Nations, Wokeness, Ukraine, foreign aid, the CIA, Jewish people, Israel, Russia, China, Iran, Covid vaccines, DEI, immigrants, Black people and lockdowns.

The Francis Scott Key truss bridge actually collapsed when the MV Dali cargo ship collided with one of the bridge supports. Six construction workers, who were filling potholes on the bridge at the time, are presumed dead. The ship is owned by Singapore-based Grace Ocean Private Ltd, and the 22-person crew were all Indian. The ship was on route to Colombo, Sri Lanka at the time of the accident.

This did not stop people from “asking questions” about the incident, a frequent conspiracist response to major events. And though conspiracy theorists are having a hard time pinpointing exactly what conspiracy caused the collapse, the one thing they do agree on is that this incident is a “black swan event.”
The term “black swan event” has been around for decades, and is used to describe a major global event (typically in the financial markets) that can cause significant damage to a country’s economy. But in recent years, the term has been co-opted by the conspiracy minded to explain an event triggered by the so-called deep state that would signal an imminent revolution, a third world war, or some other apocalyptic catastrophe.

Man, a lot of them blame DEI, which seems to be the go-to excuse on the right wing for everything. I don’t get it, though. This ship was crewed by Indians, and the bridge, the victim in this collision, was crewed by immigrant labor, so we can’t blame the magic word “DEI” for that. Fortunately, I, a non-engineer, am here to explain the problem and how to fix it.

The bridge was clearly under-engineered. It crumpled so easily with a slight bump! Clearly, those pilings (or whatever bridge people call them — you know, the bits sticking up out of the water holding up the road) were flimsy and inadequate, and need to be built back stronger. As it is, they probably wouldn’t hold up if they were slammed by a 6-ton wrecking ball, so it’s back to drawing board, and they need to be built with the goal of standing up to the force of a 100,000 ton wrecking ball traveling at 8 knots. Easy, right? I am also not a physicist, so I will leave it to the smarter people here to calculate the amount of force it needs to resist. It’s something like , where you have to multiply and divide and solve for F, way above my pay grade.

So, yeah, just build bridges that are that strong.

I’m not sure where Wokeness or P Diddy or vaccines fit into the equation. We might need to recruit some social scientists to work on the bridge redesign team, and I’m definitely not smart enough for that stuff.

Or I could stand back and let competent people find solutions, which probably don’t involve impossibly strong structures or firing people with the wrong skin color, but where’s the fun in that?