An ugly science spat

About a year ago, there was some sensational science news: the approximate time of year that the big dinosaur killing cataclysm occurred was determined. It was in the Northern hemisphere spring. That’s kind of cool.

Paleontologist Robert DePalma speaks about the fossil evidence discovered which support the impact event believed to have wiped out most of the dinosaurs almost 66 million years ago at the Goddard Space Flight Center in Bldg 28.

Now a small scandal has sprung up, one that doesn’t change the conclusion at all, but does highlight the fact that some scientists can be colossal jerks. It seems that one paleontologist, Melanie During, came up with the evidence to support that conclusion, and talked about it with a colleague, Robert DePalma, who quickly threw together a sloppy paper to scoop her.

In June 2021, paleontologist Melanie During submitted a manuscript to Nature that she suspected might create a minor scientific sensation. Based on the chemical isotope signatures and bone growth patterns found in fossilized fish collected at Tanis, a renowned fossil site in North Dakota, During had concluded the asteroid that ended the dinosaur era 65 million years ago struck Earth when it was spring in the Northern Hemisphere.

But During, a Ph.D. candidate at Uppsala University (UU), received a shock of her own in December 2021, while her paper was still under review. Her former collaborator Robert DePalma, whom she had listed as second author on the study, published a paper of his own in Scientific Reports reaching essentially the same conclusion, based on an entirely separate data set. During, whose paper was accepted by Nature shortly afterward and published in February, suspects that DePalma, eager to claim credit for the finding, wanted to scoop her—and made up the data to stake his claim.

Well, yuck…but on the bright side, independent corroboration of the conclusion is a good thing, right? Not so fast.

After trying to discuss the matter with editors at Scientific Reports for nearly a year, During recently decided to make her suspicions public. She and her supervisor, UU paleontologist Per Ahlberg, have shared their concerns with Science, and on 3 December, During posted a statement on the journal feedback website PubPeer claiming, “we are compelled to ask whether the data [in the DePalma et al. paper] may be fabricated, created to fit an already known conclusion.” (She also posted the statement on the OSF Preprints server today.)

The plotted line graphs and figures in DePalma’s paper contain numerous irregularities, During and Ahlberg claim—including missing and duplicated data points and nonsensical error bars—suggesting they were manually constructed, rather than produced by data analysis software. DePalma has not made public the raw, machine-produced data underlying his analyses. During and Ahlberg, a member of the Royal Swedish Academy of Sciences, question whether they exist.

DePalma refuses to release the raw data, which is a big red flag. Also another big problem: DePalma literally owns the site with all the fossil data!

DePalma holds the lease to the Tanis site, which sits on private land, and controls access to it.

I find that disturbing. He bought up the lease and controls who has access to the specimens and data? I can’t be the only one who finds that troubling. Maybe he’s a hero who snatched it up to protect it, and lets anyone who asks do research there, but then…uh-oh, another ugly revelation. Someone who knew him well for many years has come out to say that he’s a creep.

DePalma has a different perspective on the whole affair, but the timing of publication and the fact that the paper has many errors and that the raw data is hidden away leaves me suspicious. Also that he is trying to turn the tables and claim that During stole his ideas.

DePalma characterizes their interactions differently. He says his team came up with the idea of using fossils’ isotopic signals to hunt for evidence of the asteroid impact’s season long ago, and During adopted it after learning about it during her Tanis visit—a notion During rejects. After his team learned about During’s plan to submit a paper, DePalma says, one of his colleagues “strongly advised” During that the paper must “at minimum” acknowledge the team’s earlier work and include DePalma’s name as a co-author. DePalma says his team also invited During’s team to join DePalma’s ongoing study. “During the long process of discussing these options … they decided to submit their paper,” he says.

Collaboration and open communication are an essential part of the scientific process. This whole conflict would go away if the data, and the field site, were shared openly, but someone seems to be hoarding all that. It’s a shame, too, that such interesting work and such a spectacular fossil site are being tainted by this ugly possessiveness and grubbing for priority.

Pretty virus

What do you think? Should I show my cell biology students this 7 minute video before they go off to congregate with their disease-infested families for Thanksgiving?

That’s so beautiful and the sequence of steps so intricate that I’m impressed, even if it is trying to kill me. The video also demonstrates a lot of the cellular phenomena we’ve been talking about in class!

Triple nipple pubs!

One never knows where research might lead, and I’m not going to disparage work that attempts to quantify what seems to be a trivial and obvious conclusion. I do find it weird that such work can justify three (3) published papers, though, even if the three do have clearly different goals. Welcome to the world of women’s erect nipples.

The Point of Nipple Erection 1: The Experience and Projection of Perceived Emotional States While Viewing Women With and Without Erect Nipples

Given the research that suggests men attend to nipples and that nipple erection is triggered by sexual excitement (among other triggers), we questioned whether men see nipple erection as a sign of sexual interest. Our findings indicate that men (but not women) see women as sexier when they have nipple erection and also see themselves as sexier, supporting the idea that nipple erection is perceived signaling arousal or sexual interest.

The Point of Nipple Erection 2: The Effect of Nipple Erection on Intended and Expected Altruism

This study shows that men are more likely to do things for sexualized women, in this case, women with nipple erection. Women, however, would prefer to avoid women with nipple erection socially. This can have implications for sex and dating strategies, and female interaction in social settings.

The Point of Nipple Erection 3: Sexual and Social Expectations of Women With Nipple Erection

Nipple erection is a cue that triggers sexualization and objectification of women; women with nipple erection are thought of as less intelligent, less moral, and more promiscuous by both men and women. Women cannot control their nipple erection, yet these data show that it is used by men and women to make presumptions about women’s character and behavior.

I don’t usually notice such things because, you know, clothing, and it seems to me that clothing choice might be a stronger signal for all the things measured than involuntary smooth muscle contractions. Also, here in Minnesota, it might be more a product of being cold.

Then I read the methods. All three papers were based on a variant of this detail from the first paper.

Eighty-five men (average age 22.6 years,SD 7.33) and 355 women (average age 20.7years,SD 3.79) were surveyed. Participants were primarily White (83.4%) from a regional public university in the northeastern United States.

I recognize the pattern. Psych 101! You recruit the students from an introductory psychology course, give them a survey-based procedure, and then stat the hell out of the numbers you get. It’s the laziest kind of psych study. You’re quizzing young men and women about erect nipples in this case, and probably had no shortage of volunteers.

Then you publish it in a journal titled “Evolutionary Behavioral Sciences”, even though it has no evolutionary implications at all, and maybe, at best, measures socialized, conventional behavior in a single population of horny college-aged students with a mundane protocol designed more for the convenience of the investigators rather than probing deeply into the basis of the behavior. Come on, psychologists, do better. At least sample multiple diverse populations before making conclusions about human behavior.

It is rather depressing that one result is that showing signs of arousal is interpreted to mean a person is less intelligent and more promiscuous. Human beings, do better.

When (and how) does individual variation arise?

As anyone who has ever raised aquarium fish knows, they’re all different. Maybe you think a fish is just a fish, not very different from one another and all rather stupid, but I spent years sitting next to tanks of zebrafish, and I can tell you you’re wrong. I’d watch them gamboling about, and you’d quickly realize that oh, that one is aggressive, that one likes to hid, that one gets the zoomies and darts about the tank. You can learn to recognize individual fish by their behavior.

I always wondered about that. These were highly inbred animals, with only slight genetic differences between them, but could those little genetic variations account for strong differences in behavior? Then I acquired a new line of zebrafish, one that was the product of hybridization between our inbred lines and wild-caught native stocks, and oh boy, their behavior was radically different, instantly distinguishable. Maybe it is genetic. Maybe? I never did a formal, rigorous behavioral experiment, so I don’t know for sure.

But now a new study comes along that does what I would have been excited to know about 20 years ago (and I still am!). This is an analysis of The emergence and development of behavioral individuality in clonal fish, and it’s a bit surprising. Laskowski and others are working with the Amazon Molly, a small tropical fish that reproduces clonally, producing clutches of babies that are all genetically identical to each other — so even better than my old zebrafish — that can then be separated and raised apart from their mothers and siblings. This rules out the possibility of genetic differences causing individual differences, and leaves us to consider alternative sources of variation.

To determine the causes and mechanisms that can generate behavioral individuality in the absence of genetic and environmental differences, it is essential to first pinpoint when behavioral individuality emerges and how it continues to unfold after emergence. Birth marks a critical time point: if individuality is present at birth, this points to pre-birth influences––such as epigenetics, maternal effects, and/or pre-birth developmental stochasticity––as being key drivers of individuality. Alternatively, it could be that individuality primarily emerges after birth. This emergence could happen both gradually throughout early life, which would suggest that individuality is driven by positive feedbacks between behavior and the internal and/or external environment, or abruptly at particular points early in life, if it is linked to critical sensitive windows.

So if cloned fish are behaviorally identical to one another at Day One, but become different later on, that suggests the differences are generated by varying experiences over time. If, on the other hand, the genetically identical fish are different on Day One, that suggests that pre-birth factors (I’d lean towards favoring developmental stochasticity, just random variations at the cell and molecular level) generated the variation.

To cut to the conclusion, Amazon mollies differ on Day One, with all that implies.

I think their chosen behavior is a bit simple, they’re just looking at mean swimming speed — does a fish have the zoomies, or is it a calm quiet little guy? — which is fine, since they do get an early difference. They also used motion analysis software, so I presume they could go back and reanalyze the data for more subtle differences, but they got their answer with just one parameter. They also looked for other possible correlations.

Individuality is present at day one after birth and is not explained by differences in maternal identity or body size.

Repeatability of median swimming speed at hourly intervals on the first day after birth (A); each line represents one individual (N = 26). Maternal identity (B) did not explain variation in swimming speeds among individuals. Small and large points indicate the hourly (i.e. 11 data points per individual) and daily median swimming speeds, respectively, of individuals from each mother on day one after birth; see also Table 1. Behavior on day one after birth (C) was not related to an individual’s total length on their first day of life; see also Supplementary Table 3. Small and large points indicate hourly and daily median swimming speeds for each individual respectively; gray lines indicate posterior estimates for the effects of body size on behavior. Throughout, lines and points are colored according to the individual’s behavior in hour one on day one (yellow represents higher swimming speeds; purple indicates lower swimming speeds).

In panel A you can see that there was a huge amount of individual variation in swimming speed. In B, different mothers all produce progeny with a wide range of behaviors. That one has me wondering, though: Mama a’s babies were all a bit on the sluggish side. If they raise a second clutch from Mama a, does the second set exhibit a range of behaviors similar to that of the first set? Is there any genetic bias at all in this behavior?

Panel C shows that there was also variation in body length on Day One, which doesn’t surprise me at all — developmental stochasticity again. Body length is not a predictor of swimming speed, though, these seem to be unlinked variables.

Another feature of the study is that they observed the fish longitudinally, over 10 weeks of development. Variation increased, which would surprise no one, and it was correlated with Day One behavior. Zoomy fish stayed zoomy and became even more zoomy, while slow fish generally stayed slow for their life.

Individuality increases gradually throughout the first 70 days of development.

The predicted values of median individual swimming speed diverge over time (A) leading to gradual increases in the among-individual variance and hence repeatability (B, not shown here) of behavior. These models included only the 26 individuals on which we had complete data for the first 10 weeks of life to ensure that absolute levels of variation would remain comparable over time. Individual lines in (A) are colored according to their predicted behavior in week 1 with yellow indicating greater swimming speeds and purple indicating lower swimming speeds.

What have we learned?

Evidence is accumulating that even genetically identical animals reared under near identical conditions develop behavioral individuality, yet little is known about when exactly these differences emerge during ontogeny and how they continue to change during early life development. We show that genetically identical individuals already exhibit substantial behavioral individuality on their first day of life, highlighting pre-birth influences as being of critical importance to initializing durable behavioral differences among individuals. Epigenetic and maternal effects mediated through mechanisms such as changes to DNA methylation patterns or differential resource or hormone allocation, could influence the phenotype of offspring.

I’m still intrigued by the role of chance in development and evolution.

Another non-mutually exclusive hypothesis is that the behavioral variation we observed is the result of developmental stochasticity, that is, stochastic variation in any molecular, neurological or physiological markers that occur over ontogeny. An intriguing possibility is that the phenotypic variation we observed here––whether arising from epigenetic, maternal, and/or developmental stochasticity effects––might itself be adaptive, for example, as a potential bet-hedging strategy. Generating phenotypic variation among one’s offspring by such non-genetic means might be especially relevant in clonal organisms such as the Amazon molly. There is, for example, evidence in clonal fish, and poecilid fish specifically, that DNA methylation mechanisms and developmental plasticity more generally might be especially sensitive to environmental influences, offering a mechanism through which mothers can generate variation among their otherwise genetically identical offspring.

Developmental stochasticity as part of an evolutionary bet-hedging strategy sounds like an interesting model, and probably important in species like fish (and spiders!) that pump out huge numbers of offspring with concommitant high likelihood of death.

This kind of behavioral analysis of organisms with limited genetic variation is one motivation for what I’m doing in the lab — taking the offspring of one spider parent and then inbreeding them over multiple generations to reduce genetic variability in one lab population. A couple more generations, and then it’ll be time to work out some behavioral assays to identify differences that we can select for. Swimming speed won’t be one of our parameters, though. Not even speed in general, they tend to all be quiet lurkers. Web configuration, aggression, pigment patterns, though, those are all candidates for analysis down the line.

Humanity’s imminent, mysterious extinction

You want something more to fear? Try this on for size.

Across the world, there’s evidence that spider populations are in danger of collapse. A landmark 2019 study in Nature found that the number of spiders, insects, and other arthropods dropped precipitously in Germany from 2008 to 2017, with the total number of different species researchers counted declining by 33 percent and total biomass dropping by 40 percent. Remember the Australian trapdoor spiders I told you about? They’re disappearing, too. After a century of settlers clearing land for crops and raising livestock, they’re becoming harder and harder to find. It’s all but certain that entire species of spiders will go extinct before we even have a chance to discover them, falling victim to industrial agriculture, pesticides, and climate change.

Then there’s this:

Alaska canceled the snow crab fishing season for the first time on Monday, as crab populations mysteriously plummet.

An estimated 1 billion snow crabs suddenly disappeared from the Bering Sea, according to CBS News. The collapse deals a heavy blow to Alaska’s biggest crab industry, and could drive many fishers out of the business.

“Mysteriously.” What a useful word. We send out trawlers to shred the seafloor, we drop traps and snatch away millions of crabs, and we spew garbage and microplastics into the ocean, and then shrug and say it’s a mystery why populations abruptly and catastrophically crash.

Another example: we’re seeing fewer vehicles with dead bugs splattered all over them.

From 1996 to 2017, insect splatters fell by 80 percent on one of the routes Moller regularly travels. On the other, longer stretch, they plunged 97 percent. Conventional measures show similar trends, and more recent observations have seen even sharper declines, Moller told us.

This article takes the somewhat interesting approach of speculating about alternative causes — which is fine, they’re being thorough, but we’re eventually going to have to face the reality that something “mysterious” is also happening to insect populations.

So, given this uncertainty, isn’t it possible that our spookily clean windshields are caused by factors other than rapidly declining insect populations? After all, we still see bugs everywhere, we just don’t seem to mash them with our cars as much.

Many smart people we spoke with, including entomologists and wheat farmers, speculated that maybe the cars have changed, not the bugs. As vehicles become more aerodynamic, the thinking goes, their increasingly efficient airflow whisks the bugs away from the windshield instead of creating head-on splatters.

Um, no. That’s a very silly explanation, as the experts they consult state, but also for obvious reasons. Car grills have not become more aerodynamic, nor have radiators. Also, the cars…or rather trucks people are driving are not particularly sleek. In fact, the trends are for more aggressively blunt, large, flat front ends. A lot of column inches get wasted on this ridiculous hypothesis, which can also be dismissed experimentally.

But we also saw 60 percent declines in insects between 2004 and 2021 in a British study from the Kent Wildlife Trust, which built on a Royal Society for the Protection of Birds effort in which thousands of people used “splatometers” to measure bug splatters on license plates, which aren’t much affected by aerodynamic advances elsewhere.

So then we get another off-the-wall hypothesis. It’s not that insects are in decline, it’s that there are fewer insects splattered by individual cars because we’ve vastly increased the number of cars on the road. I’m losing patience with their efforts to find any explanation other than that we’re poisoning the environment, but OK…being thorough is good.

Americans now drive three times as many miles as they did in 1970, and the explosion of trucks and SUVS means many of us do it in cars with much, much larger windshields. Back-of-the-napkin math suggests acreage of windshields out on the American road has tripled. And that’s probably an underestimate in some places: A large majority of our increase in driving has come on a narrow set of major urban roads, according to our analysis of Bureau of Transportation Statistics data. And as Kenny Cornett of design-software giant Autodesk points out, more traffic means more vehicles riding in each other’s bug-free aerodynamic slipstreams.

So in our little thought experiment, which makes the depressingly accurate assumption that bugs are a finite resource, our bugs-per-windshield metric would have been cut by two-thirds even if the number of bugs had remained constant.

I…I don’t even. This would only work if, instead of sampling a tiny fraction of the extant population with our windshields, we were exhaustively extracting enough bugs with one car to deplete the population for the next car. If that were the case, then maybe tripling the number of cars would be responsible for the population crash. But that’s not the case. The column of insects wiped out by the passage of a car is minuscule compared to the population in the fields, over the lakes, around our homes.

Treating the excessive driving habits of Americans as a rationalization for insect extirpation rather than as part of the problem is troubling, too.

Weirdly, the article concludes that the problem may not be as big as we think because…we have so many cars?

So, simple math hints that the very real ecological disaster of the collapse of insect populations may look even more apocalyptic thanks to the parallel rise of another ecological time bomb: the world’s intensifying love affair with ever more and ever bigger automobiles.

No. This makes no sense. We’ve got other methods of sampling insect populations that are not bug-splatters on cars. When I first moved to the Midwest, a regular feature on the news was when vast clouds of mayflies and midges would hatch out and rise from our lakes to appear on weather radar. Nope, not so much anymore. I would go outside and marvel at the dense masses of flying insects that would cluster around streetlights — nowadays, all summer long, the lights are lonely and shining into an emptiness. I wanted to use spider populations as a proxy for insects, and spiders aren’t leaping in front of cars on the freeway…and see the first article cited, they’re in decline, too.

What’s going on? Oh, I know the answer: it’s something “mysterious”. Problem solved.

Don’t worry, though. We don’t even like bugs, so who cares if they disappear. Then, when they’re gone, the birds and fish and reptiles will fade away, but they’re not our pets, so who cares? Unexpected crop failures…well, we’ll come up with a technology to deal with that. And finally, when humans mysteriously go extinct, there will be no one left to worry about it, and all the windshields on the decaying cars we leave behind will be shiny and clean and their grills will gleam unspattered. No one will be standing around wondering what happened to all the people, and best of all, there will be no one standing around smugly to utter the non-answer, “It’s a mystery.”

I’ll miss the Pacific Ocean

Wait, no, I won’t. I’ll be long gone. I expect the human species will be extinct by then. This is entirely predictable, that thanks to ongoing plate tectonics, eventually the continents will collide into a super-continent, Amasia.

It won’t actually be named that, of course, since the hyper-intelligent spiders that evolve to replace us won’t be using English.

Biology will get interesting, though.

Surrounded by a new superocean, the newly formed supercontinent will also have decreased biodiversity.

“Earth as we know it will be drastically different when Amasia forms. The sea level is expected to be lower, and the vast interior of the supercontinent will be very arid with high daily temperature ranges,” Li said. “Currently, Earth consists of seven continents with widely different ecosystems and human cultures, so it would be fascinating to think what the world might look like in 200 million to 300 million years’ time.”

It’ll be a harsher world in many ways, but at least it won’t have Homo sapiens screwing it up further. Also, you might want to start getting on the good side of the hyper-intelligent spiders.

It’s Nobel week, and paleogenomics wins!

First up, look who won the 2022 Nobel in Physiology or Medicine: it’s human evolution! As represented by the paleogenomics work of Svante Pääbo, who has been recovering ancient genomes, digging up old Homo sapiens and Neandertals and Denisovans.

I do have one reservation, though: the Nobel announcement claims “the ultimate goal of explaining what makes us uniquely human.” I don’t think we can accomplish that by decoding genome sequences. Identifying the different ancestral groups that led to us is interesting and informative, but let’s not get hung up on just DNA.

Poor Dimorphos

It’s just an innocent space rock, didn’t do anyone any harm, but NASA is getting ready to practice its marksmanship and shoot at it from a distance of 7 million miles. It’s getting hit tonight, so you can watch the livestream of the sniper shot right now.


Not the view you want to see through your windshield.

Frantically rewriting lectures

Aaargh, neglecting the blog again. My big distraction today: as always happens, I looked over last year’s notes and grumped at myself and said this will not do, this is totally inadequate, I need to rewrite the whole thing. The plan for tomorrow was to talk about the pentose phosphate pathway AKA the hexose monophosphate shunt AKA the phosphogluconate pathway because this stuff is important and, weirdly, our textbook doesn’t even mention it, so I can’t even punt and tell the students to go away, don’t bother me, just read Chapter X. As is common in cell bio, all we talk about is how we burn sugar to make ATP, and very little about essential anabolic reactions. And that bothers me.

The PPP is cool beans, too, so I rewrote the lecture from the ground up to cover more of the details, expanding what used to be a short aside into the whole dang talk, and I’m probably going to terrify them all with a peek into more advanced biochemistry (this is a class for 2nd year students, so it’s introductory level) and the way all of biochemistry is tangled and intertwined, but hey, they’re smart students. They can take it.

Unfortunately, it’s stuff that isn’t going to entertain a more general audience, unless you think filling in the details on this introductory slide would get you excited.

Man, I was so into biochemistry as an undergrad, and then I got distracted by neuroscience and development. I need to begin a second lifetime so I can catch up.

Now I have to finish grading, which is far less enthralling.