I wonder what happened to the coward who attacked Jey?

Jey McCreight is an old friend I’ve known since they were a an undergraduate studying biology in Indiana. I’ve been happy to see their accomplishments over the years: grad school, a post-doc, landing a job at 23andMe as a genomics expert. They were also an activist in the atheist movement — Jey was one of the minds behind Atheism+, and we all know how well that effort to incorporate more humanism into atheism went. Now they are still an activist, founding the organization BeyondXandY arguing that biology is nonbinary and that people are more than their chromosomes. Jey clearly is bold and optimistic enough to take on noble causes in spite of all the haters, and doing the right thing as a trans man has got to be one of the braver things they have done.

Last month, this happened:

McCreight said they had been advertising the event with flyers across the city that included their photo and had also appeared in the local LGBTQ+ publication, Windy City Times. They assume the event’s publicity is how the attacker recognized them.

“I’m telling this story now because I’m finally in a place where I can talk about it without really freaking out badly,” McCreight said, explaining that there are still a lot of gaps in their memory of that night, but they think they were walking home alone from getting food.

The attacker asked if they were McCreight, and McCreight cheerfully confirmed, assuming it might be someone who appreciated their work.

“He very quickly pushed me to the ground and started repeatedly punching me in the eye,” McCreight said. “Afterward, I thought he had maybe hit me with a brick or something because it was so painful. I had never been beat up before in my life.”

McCreight said the attacker also used a pocket knife to cut them all over their body, but not deep enough to leave permanent damage.

“It was very scary. He even tried to strangle me briefly with something that thankfully didn’t work well and just kind of left an abrasion on my neck.”

McCreight said they don’t remember how they got away or if the person eventually just let them go. But somehow, they got home. It took them over a day to realize they needed an ambulance because they were in such a daze.

But on May 1, McCreight recounted, they realized they needed help. An ambulance took them to Chicago’s Advocate Health Center, where they said they received excellent care, which included emergency surgery on their eye. After that, it took weeks for their vision to return to normal.

“I think it’s really important for people to know that this is the reality of being trans in the United States,” they said. “I’m a non-violent nerdy cat guy who likes talking about science and wants to be the next Bill Nye, and because of that, someone basically tried to kill me or at least beat me up bad enough to scare me into silence.”

They said for a little bit, they considered giving up their public-facing activism in the wake of the attack. But then, hospital staff of all kinds – from doctors to nurses to the people bringing them meals – all learned about McCreight’s work and told them to keep going.

“They all told me not to give up on my dream.”

Horrifying. That some guy would just turn and attack a friendly, nerdy fellow walking down the street because they are trans is appalling. Listen to them telling their own story, and support BeyondXandY.

I have been replaced

I’m a bit frustrated — this stupid knee doesn’t allow me to walk on rough ground. I can handle floors and sidewalks, but this part of my yard where Mary has been planting new berry bushes is mostly inaccessible to me. Yesterday, Mary tells me she has spotted some interesting new spiders on the leaves. Can I come look? Not without risking a fall.

It would be a bit much for me to hand her my Canon D8 with the 100mm macro lens, so instead I gave her a clip-on magnifying lens for her iPhone, which she was already comfortable using, and she went off into No Man’s Land and got a bunch of very nice photos of these tiny (less than 3mm) guys, and left me feeling useless.

Anyway , what she had found was a lot of meshweavers, small spiders that put down sheet webs, which they use to catch smaller prey, like aphids and leafhoppers. Meshweavers are a gardener’s friend, so it’s good to see them hard at work protecting our raspberries. This is a dwarf spider, also called a money spider:

And this is a pair of dimorphic meshweavers. One species, but males and females look dramatically different.

Clearly, it’s time for me to hang up my pretense of being an arachnologist and teach Mary how to use the D8. I’ll just park myself in a rocking chair on the deck and watch her have all the fun.

Don’t ask me for diet advice

Oh no. I have been asked for dietary advice.

I am not qualified. I’ve never taken a nutrition course, I have no degree in the field, you should not take nutrition advice from me. That’s the simple answer.

On the other hand, I’m aware of the problem: there are unholy swarms of people and ‘influencers’ who have less knowledge of basic biology than I do who are flooding the zone with all kinds of cockamamie ideas based primarily on ideology. Sometimes the people who pretend to have the most knowledge about the human body give the very worst advice, so how do you figure out what is good advice? I mean, you’ve got total wackaloons who have driven themselves into induced comas and neurotic breakdowns telling you to eat nothing but beef; you’ve got other nerds insisting that everyone must avoid meat, eggs, and gluten (which is necessary for some people); and then you’ve got breatharians and other insane people who believe in living on diet Coke and Big Macs.

On the third hand, human beings have survived for hundreds of thousands of years without TikTok, eating what was available and tasted good, and cultivating wonderful cuisines without relying on bizarre notions of what some wild-eyed skinny fanatic said. That’s the thing about nutrition: traditions are good guides because they’re the product of people who survived their diet. OK, French sauces and hakarl might be extreme and bad for you in the long run, but human experimentation also gave us curries and bread. We haven’t died of anything like that unless consumed in excess.

My general guide to eating is simple: moderation in everything. Avoid heavily processed foods. Try a variety of things, a ‘balanced’ diet. Beans, rice, and potatoes can be the solid foundation for your diet, and have the additional virtue in these tight economic times of being cheap. Build on them with spices — I feel like one of the cardinal sins of the American diet is the spice deficiency. Spices make mundane, boring, but reliable staples interesting and allow you to get flavor without feeling like you have to indulge in buying exotic, expensive, heavily processed foods.

Add stuff you can find in season. I like to add a piece of fish to a meal for a bit of richness…or use an egg, or some broccoli, or a side of peas. Avoid uniformity.

Learn how to make a paella, or a curry, or a stew. Just the process of assembling all the elements of these kinds of foods guarantees that you’ll get a dietary variety, and it will taste good. I trust tradition far more than I do the latest influencer fad. Your best bet is to ignore people like me and just spend more time in the produce section of your grocery store, gathering up tomatoes and turnips and cabbage and mushrooms and carrots and peppers and onions and cauliflower and green beans and garlic, and then figure out how to cook them and make a delicious meal. Pick up a variety of fruits for dessert.

It takes a bit more effort than picking up a box of premade something-or-other, but it would be better for you.

This too shall pass

A little bit of good news: Trump’s name might get chiseled off of his attempts at immortality soon. A judge has ruled that the Kennedy Center should have its good name restored.

US district judge Christopher Cooper, Trump noted, had ruled that his handpicked board members, who “unanimously voted to add the name ‘TRUMP’ onto the former Kennedy Center, making it The Trump Kennedy Center, did not have the right to do such an addition, and the name, ‘TRUMP,’ must be removed”.

He mad. He has to know that once he is inevitably out of power (preferably by being hauled out on a stretcher), all his vainglorious attempts to scribble his name all over everything will be eradicated.

So we can also hope that eventually his mad rulings about vaccines, at the behest of his brain-worm infected buddy, RFK jr, will be erased in time. So look at this executive order to strip children of protections with a grim sense of happiness deferred.

An executive order signed by Donald Trump with little fanfare on Friday could have a huge impact on the health of US children, as it instructs the Centers for Disease Control and Prevention (CDC) to cut the number of recommended childhood vaccines almost in half.

The vague language of the order, which refers to “a scientific assessment that compared United States childhood immunization recommendations with those of peer nations” published in January by anti-vaccine activist Robert F Kennedy’s health and human services department, does not explicitly state that the new recommendation removes vaccines against seven diseases from the schedule.

The assessment, co-authored by the subsequently fired vaccine skeptic Dr Tracy Beth Høeg, concluded that the CDC director should update the childhood immunization schedule “to keep vaccines for 10 diseases – measles, mumps, rubella, polio, pertussis, tetanus, diphtheria, Haemophilus influenzae type B (Hib), pneumococcal disease, and human papillomavirus (HPV) – for which peer, developed nations share international consensus, as well as varicella (chickenpox) … in the category of vaccines recommended for all children”.

Implementing that recommendation would mean removing vaccines for these diseases from the recommended schedule:

hepatitis A
hepatitis B
meningitis
rotavirus
influenza
Covid-19

The assessment also recommended cutting the number of doses of the human papillomavirus, or HPV, vaccine from two or three (depending on the child’s age) to one.

Someday the proper medically-informed schedule will be restored, and we can celebrate that. Someday. For now, we just have to deal with the suffering and death of a few babies. We just have to wait until the light is restored.

(I’m actually not going to celebrate until RFK jr is prosecuted for crimes against humanity, or his mangy rotting corpse is buried deep in the ground, whichever comes first.)

Eat and live

I’ve been a distracted mess lately, with all this PT stuff as well as a week of administrative malarkey, but I did notice a a provocative comment that I feel compelled to respond to.

Upon accepting the risk of dispensing an unpopular remark: One day, we shall have to set nature in order using genetical engineering.

No creature should devour any other.

Wow. That makes no sense. We humans are obligate heterotrophs — we must obtain certain vital molecules by consuming other organisms. For example, we cannot synthesize valine, isoleucine, leucine, methionine, phenylalanine, tryptophan, threonine, histidine, or lysine, so we have to consume other organisms that contain those substances, or we die. I guess we can define “creature” to escape the problem, which is the vegetarian solution. We don’t eat meat from animals by making the decision that plants don’t count. It’s very convenient to say that killing carrots or yeast or lettuce is ethically OK, but if you think about it all deeply, even a carrot is a product of processes that kill insects with pesticides. Do insects count? What about protists? The lines are all arbitrary and we each draw our own lines.

Is our solution to genetically modify humans so they can synthesize every molecule we need? Or are we going to build factories to create all these essential substances as supplements?

But deeper still, the planetary biome is built on dependencies contingent on death and consumption, in every food web that exists. For example, sea otters eat sea urchins; sea urchins eat kelp; when sea otters are eliminated, the kelp forests die. How do we genetically engineer “devouring” out of the system without necessarily deleting entire ecologies? The only way any of this can happen is by magic.

Nature is already in order, reordering it to your preferences is silly.

Shouldn’t a president be mildly aware of the world around him?

Here we go again. Trump’s idea of diplomacy is a sane person’s idea of bullying.

Donald Trump has threatened to “blow up” Oman if it fails to “behave” in a casual aside during a cabinet meeting, as the US scrambles to reopen the strait of Hormuz.

I had two students from Oman this past semester. One of the things I, a mere college professor, do is look up my students’ backgrounds to avoid saying something stupid and insensitive, like “we should blow up your home”. If only our president were a tenth as aware.

SHUT THE FUCK UP, DONNY.

I choose not to be optimistic

I see a lot of online commentary anticipating that Democrats will flip the house and maybe the senate. They’ve been encouraged by the nomination of Ken Paxton, a totally repulsive corrupt sleazeball, to run against James Talarico — the idea is that that is going to weaken the Republican vote in Texas, along with other visible factors.

Over the last several days, I traveled 550 miles through trump country in Wisconsin, Iowa and Minnesota. I have reliable information that this route was once replete with Trump shrines, but on this trip, there was one (and it was a doozy, near Effigy Mounds, Iowa). All the others had vanished some time over the winter. This isn’t Texas, but it is a very MAGA landscape, and thus a good an indicator. In at least one case, the former Trump Shrine had over the years displayed anti-abortion and various jingoistic symbology. All that stuff was still up, but the name Trump had been taken down. The point is: right wingers, even hard MAGA level right wingers, are erasing Trump from their rhetoric. Assuming that this is a national phenomenon, it matters in Texas.

And now, with the odious Paxton being put in place of the more mainstream Republcian Cornyn to run for Senate in Texas, owing to Trump loyalists following his endorsement, most observers who know Texas are saying that this seat is in play. According to The Hill, “The nonpartisan election handicapper Cook Political Report shifted its rating of the Texas Senate race toward Democrats on Tuesday from “likely Republican” to “lean Republican,” after state Attorney General Ken Paxton defeated Sen. John Cornyn in the marquee race’s GOP runoff.” Read that carefully. They are not projecting a Democratic win, but they are saying the race is in play.

I’ve seen fewer Trump signs in my area, too, but I can’t help but note that a majority of those Texas Republicans voted for the Trump-endorsed candidate anyway. I have seen predictions of the ‘blue wave’ for years, and every time, I’ve been disappointed. I refuse to fall for it anymore. I predict minimal change as a consequence of the midterms.

Greg Laden is only slightly more optimistic than I am.

There are strong indications that many Republican-held House seats are likely to flip over to the D column. There are reasons to hope for a slim Democratic majority in the Senate. The chances that Republicans will hold trifecta power after the new crop of electeds is planted in January is about zero. Will Texas be part of that important, historic, and civilization changing moment?

To answer that question, I refer to fashion and style guru, Melania Trump. I’d love Texas to get on board, but we don’t really need texas, and Texas always disappoints. For mere self preservation,

I could be totally wrong, and I hope I am, but I expect the Republican party of Evil will cling to their death grip on American politics for a few more years, simply because the electorate have convinced me that they’re morons.

An epic humble brag

Liang Cheng is an oncologist a Brown University. I’d never heard of him before, but I am told that he is incredibly famous by Liang Cheng, as he announced himself on LinkedIn.

I am deeply humbled and grateful to learn that my H-index has now reached 140. I was also honored to see that I am currently ranked among the two most-cited researchers worldwide in the fields of Urologic Oncology and Urology on Google Scholar.

In addition, my i10-index has reached 1060; that is, one thousand and sixty publications each cited at least ten times. I was told that this may represent a world record – what an extraordinary honor!

Nonetheless, these numbers are far less important than the people, mentorship, friendships, and collaborations behind them. This milestone is truly a triumph of team science. I owe immense gratitude to my mentors, colleagues, collaborators, residents, fellows, medical students, and friends who have inspired and supported me throughout this journey over the past two decades.

Academic medicine is never an individual accomplishment. It is ultimately about advancing science and medicine, educating future generations, and improving patient care. If our work has contributed even in a small way toward those goals, then I feel extraordinarily fortunate and grateful.

Thank you for being part of this journey. The best is yet to come!

I hate to be the one to tear him down, but no one cares about your H-index and i10-index except, maybe and importantly, administrators and fellow H-index chasers. Anyone else remember that scene in American Psycho where Patrick Bateman and several of his cronies are comparing business cards, noting the quality of the stock and the embossing and the inks? Yeah, that’s what it’s like seeing someone brag about their indexes. Don’t care.

It’s also because those numbers are thoroughly gamed. I looked him up on PubMed, and it’s true, his name is on a lot of papers: papers that have 10 or 20 or more authors, and there he is, somewhere in the middle of a sea of names, rarely first or last. He really does owe a lot to his “mentors, colleagues, collaborators, residents, fellows, medical students, and friends” who have been tacking his name unto their papers! And further, his publication rate, that is, the rate at which his name gets plugged in to a long list, is approximately a paper every two days, which is insane. This is authorship by rubber stamp.

I think it is valid that many research endeavors nowadays require a large team, and he may have been an indispensable member of such a team, but then to use that cooperation to brag that he is #1 or #2 in his field is unseemly. It’s also dangerous, Dr Tall Poppy. He was spamming his ‘accomplishment’ on every social media site he could find, and on Xitter, Michael Eisen noticed.

The author’s Google scholar profile falsely lists multiple papers that he didn’t author, and therefore the citation count and h-index are inaccurate.

Whooops.

I do enjoy seeing a braggart taken down a peg, but Liang Cheng is a symptom of a greater problem: we’re drowning in artificial metrics, amplified by AI slop.

Over the last few decades, science has undergone a “citation revolution.” Scientific life used to be structured by personal reputation and mutual acquaintance; now it is defined by quantitative assessments derived from citations.

And this reward system has warped scientific life in dramatic ways. It has resulted in the obvious and widespread gaming of citation metrics; but, more insidiously, it has pushed scientists toward risk-averse, incremental, and above all unambitious research. The logic of institutional science has become increasingly divorced from actual knowledge and discovery. In a system governed by these perverse incentives, the inevitable endpoint is simply AI-generated slop at scale.

Now, with AI, we’ve built a remarkable new technology that opens up dramatic new horizons for scientific work. But we’re deploying that technology within an institutional structure that incentivizes, above all else, the maximization of metrics that don’t have much to do with real science. The underlying problem is not with AI, but with the institutions and incentives that define modern science.

That is an excellent article, everyone should read it. It actually ends on a promising note, regarding AI as a tool that could break us out of the dead-end, grasping competition for a magic ranking number, as exemplified by the case of Liang Cheng.

The citation index was designed in the 1950s and ‘60s as a solution to the information crisis engulfing scientific life. It ended up becoming much more than that: a regime that reshaped what science was, how it was rewarded, and what kind of science got done. Now that regime is collapsing under the weight of its own contradictions. I think it’s a fantastic opportunity to build something better.

No bread for you, only circuses

In June, the White House will host a UFC fighting event. They’ve already torn out the White House lawn, are building a giant fighting cage to hold all the lights and cameras, and will be placing the Octagon in the center.

It’s historic, don’t you know. Bulbous sweaty men kicking each other in the face is considered a dignified way to celebrate the 250th anniversary of the United States…and it’s not political, it just happens to be held on the president’s 80th birthday.

The president promises us it won’t cost the American taxpayer a thing (I’ve heard that somewhere before). It’s all paid for by special ticket prices — this is not a public event — and sponsorships from Paramount and a crypto company. I’ve never watched UFC, is it all scripted kayfabe bullshit? If so, that would be perfect.

Canadians, Europeans, everyone living in the civilized world outside our borders: are you laughing at us? Because I feel like hiding in shame for some reason.