Pinned toot

Hello, all. I’ve been around for a few days but haven’t yet made an post. So here we go.

I’m a consultant with The Bioinformatics CRO working on a variety of small and large projects ranging from fundamental genomics to clinical decision support. Before that, for several years I was a postdoc and ORISE fellow specializing in high-altitude medicine and physiology at the University of Colorado Altitude Research Center. My academic background is a nearly even mix of , machine learning, and biology.

The ARC* has been sadly moribund for a few years, but thanks to collaborations with other groups, we’re starting to get more active again. Hopefully I will have more to say about that in the future. Meanwhile, feel free to ask me anything about medicine—I think I still remember most of it.

Years before that, I was an Air Force (after a brief stint as an Army infantryman) followed by a couple of years as a civilian EMT. My time in patient care informs my approach to science: the numbers I crunch represent human lives.

Otherwise, I’m an armchair hoping to be able to call myself an amateur paleontologist again one of these days—by which I mean actually spending some time in the field and/or the prep lab—a too-occasional science fiction writer, and chronically sleep deprived. Also, my life is the internet: it’s cats all the way down.

*Fellow fans may recognize the jacket in the picture. My wonderful fiancée found it for me when I was hired at the ARC, for exactly the reason you think.

Nothing says “hey, hot stuff!” like a fibula fracture.

Text, for anyone who doesn’t want to click the link. Every once in a while I can convince myself I’m still a writer.

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“How did the 4 years in the change your life?”

Thanks for the A2A. It wasn’t four years in my case, only two. At that time the US Army offered short enlistment for various MOSs including 11B, and fortunately I took one.

I was a mediocre infantryman, to be honest. I was very good at what are perhaps the two most important infantry skills, marksmanship and road marching—but lousy at the rest of the job. In particular, I have a poor sense of direction so I get lost in the woods easily, I don’t tolerate sleep deprivation well, and I’m terrible at throwing so I was just hopeless with hand grenades. One of my best friends was a former minor-league baseball pitcher, and an absolute wizard with grenades as you’d expect, but a really bad shot. We made a deal that if we ever went to war together, he’d give me all his ammunition, I’d give him all my grenades, and we’d stick close together.

Fortunately we never did go to war: that had to wait until Desert Storm, by which time I’d gone over to the Air Force as a medic, a job which suited me much better. Two years in peacetime humping a rucksack, burning through ammunition at the range, and moving a whole lot of dirt with an entrenching tool didn’t make me some kind of super-soldier. It was a job, with its good and bad points like any other. I was glad I’d done it, and glad to leave. The big-picture outline of my life would probably be about the same if I’d never done it at all.

But it did change me, and for the most part I think in a good way. Infantry work requires a level of endurance few other jobs, military or civilian, can match. You don’t have to be especially strong or smart or tough to be a grunt. You do have to be to determined. To keep going, mile after mile. To find what creature comforts you can in the midst of heat and cold and mud and sand. To meet the worst the world can throw at you with tempered pride and a sense of humor. To not stop, no matter how much you want to, because you won’t let your fellow soldiers down. You can whine, you can curse, you can even cry. You just can’t stop.

I’ve been through other hard things in my life since then. Working in the base ER as a medic, and then as a civilian EMT, showed me more blood and pain than I ever saw as a grunt. My divorce and subsequent romance with the bottle came closer to killing me than any enemy bullet. Getting my PhD was a very long hump indeed, with plenty of agony along the way.

Through it all, I told myself: You marched through Georgia. You can do this too. One foot in front of the other. Rest and food are over the next ridge, or maybe the next one after that. You’ll get there, because you have no other choice. Infantry.

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“So I’m curious: do you even bother drinking the at this point, or just hook it up to an ?”

Reuse as needed.

Decades ago in junior high and high school, long before something like was remotely possible, I was several times accused of for writing good essays. I understand why are so concerned about -generated . Teachers also need to understand how discouraging and overwhelming the accusation of is to who are simply doing their best.

“Oh, you’re one of those. Never mind.”

Works for about 90% of internet arguments.

are close to being gods in their domains: possibly no other in the entire have more autonomy except . It takes a lot to lead to this kind of shakeup. We’ll almost certainly never hear the details, but I admit to a great deal of morbid curiosity.

military.com/daily-news/2024/0

Seen on another site anent the prospect of winning in because sufficient numbers of and stay home or vote :

“Sometimes a little short-term pain is needed for long-term gains.”

And here is maybe the ’s biggest blind spot. There will be no long-term gains from another Trump . Zero. None. The country is not going to “wake up” en masse, eject from office at every level from Washington to the county dogcatcher’s office, and usher in a glorious new age. It. Is. Not. Going. To. Happen.

This was true in #1968, it was true in #2000, and it’s true in #2024. If there’s ever a time when it isn’t true, I don’t expect to live to see it.

But there will be a whole lot of short-term and medium-term and long-term pain. Maybe disgruntled voters with a long list of reasons why isn’t morally pure enough think they’ll live through it. Hell, maybe they’re right … which says a whole lot about their version of morality, none of it nice.

Their “short-term pain for long-term gain” is suffering and death for people I love. Anyone who’s okay with that can GTFO.

From the comments on the Facebook post where I saw this: “And yet raises prices every year to and claims it is part of their extensive process.”

I continue to believe there is value in the traditional system. Specialized , , peer review, even fees and paper copies—although really the number of paper copies needed is minimal, and subscription costs should be too. The major journals have done a lot to encourage high-quality and spread , and I hope they keep doing so for quite some time to come.

None of which means any specific journal or publisher should continue to exist, and this shows why. The system is way overdue for a serious mucking out.

This is a really good overview of current methods for () identification in . Every person who cares about which TFs are doing what (which is most of us, I suspect) should think really hard about the relative virtues and flaws of the major methods, and not lean too hard on any one of them.

Thiago Carvalho  
"A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is know...

Actual conservatives won't be the first people purged if the Nazis get into power.

Won't be the last, though. When the fascists come for them, they'll have a moment when they wonder if they should have been braver when their friends and family started to turn.

“What would your course of action be if you saw a healthy, -bodied individual get out of a vehicle that they just parked in a space?”

“A number of people close to me have invisible . They look healthy and able-bodied, but they’re really not. Their conditions are just as real and disabling as those of anyone who needs a , a , or a to get around. And their agree, which is why they’re authorized to park in handicapped spaces. Unless you have the appropriate training and have conducted a thorough examination, you have no grounds to dispute this.

“So if your course of action is to challenge them, shout at them, threaten them, or demand that they prove to your satisfaction that they’re “really” disabled … my healthy, able-bodied course of action will be to introduce you to what feels like, up close and personal. That process won’t be fun for you, but you’ll have a much greater understanding afterward, for whatever remains of your miserable life.”

Usually I try really hard to avoid being Internet Tough Guy, but there are times it’s the only possible response. Speak the language your audience understands.

Look, you either believe the concepts of and apply to platforms, or you don’t.

You can say the only applies to the , not entities—which is undeniably true—and therefore sites have no obligation to provide a platform for speech the owners of the site don’t like. This is a reasonable and defensible position.

Or you can say social media sites are the new , and therefore the owners have a moral if not legal obligation to allow anyone to say practically anything using their platforms. You can even point out that the government charters corporations, and is responsible for a lot of , so by allowing censorship in that particular environment, the government is at least complicit in interfering with free speech rights. This is also a reasonable and defensible position.

Maybe you can even try to find some kind of well-articulated middle ground between these positions, although I have to say I don’t remember ever seeing anyone do so. I think most people do hold opinions somewhere between the two, but they don’t tend to spell it out.

What they do instead is argue either side as it’s convenient, which is irritating as hell. And yes, this is a rare bit of “both sides” on my part. I see a whole lot of leftish folks, who are generally not big fans of corporate power, deploying the first position against right-wing types—while complaining about the arbitrary and often clearly biased way et al. censor left-wing statements.

The complaints are justified. Hypocrisy is not.

Just pick a position, be honest with yourself about what that position is, and stick to it. No matter where you fall on this spectrum, you have to be aware that the mechanisms of speech, and by extension the press, have changed dramatically over the last thirty years and will continue to do so. Knowing where you stand is important.

The single worst job I ever had involved no hands-on patient care at all.

Now, I experienced some very bad days as a , and more as a . I worked on , in , and in safety net . I saw suffering on a scale I had never even imagined before. Of course I did my best to relieve that suffering—both because it was my job, and because I’m a decent human being—but a lot of the time I just couldn’t, and neither could anyone else. I celebrated my successes and mourned my failures. The memory of the former sustains me to this day, but the accumulation of the latter did lasting damage to the inside of my head. Practically anyone who’s ever been in the biz can say the same.

But all the and car and and cases and long, steady descents into the grave, over the course of years, didn’t burn me out like two months in a practice.

You may wonder why. Okay, cardiology patients are generally pretty sick: you don’t get assigned a , rather than having your primary care provider take care of it, unless your ’s in bad shape. Even so, could it really be worse than all the above? After all, cardiology offices tend to be clean, well-lit, organized places. Patients have appointments. Fairly routine care, and if there’s really bad news, it’s the who have to give it—which is not the situation in , let me tell you.

Well, it did, and here’s the reason. Like I said, I wasn’t taking care of patients directly. My interaction with them was brief, in exam rooms after they’d already been checked in and seen by their providers, and I never touched them. It was all paperwork.

My job was to be their advocate with the companies. I did most of my work in an office, with a comfy chair and a phone and a coffee cup close at hand. The job was actually supposed to be an position, but I impressed them enough at the interview to get it, and I got paid more for it than any other medical job I had before or since.

I read their and , studied insurance claims, and—now we come to the crux of it—looked over the reasons those claims were denied. Sometimes very elaborate reasons, with lengthy justifications. Other times the feedback from the insurance companies was basically just “NO.”

And then I called those companies, and worked my way up through the phone tree until I got someone on the line with some actual decision-making authority, and explained to them in great detail why they should approve a particular medication or procedure that would keep our patients from dying.

I succeeded … maybe a quarter of the time? Probably less. Occasionally the failures weren’t complete: I couldn’t get them to approve whatever the cardiologist had recommended, but I could at least squeeze something out of them. Something that would keep our patients, the people entrusting us with their lives, going for a little while longer. Some sliver of hope for the patients and their families. Some human connection that reminded the people on the other end of the line that their job wasn’t actually to condemn people to death, at least not on paper.

Usually not. But often enough to keep me there for a little while. The nightmares stayed under control as long as I had a bottle waiting for me when I got home. Now that I think about it, that may have been when my drinking problem got serious, although it would take several more years to fully manifest. Good thing it wasn’t a practice, I guess.

A friend’s post dredged this memory up. I was going to leave it as a comment there, but I didn’t want to make it all about me. They have enough of their own problems. Just know, if you’re fighting this particular war right now, I’m with you.

Oh yeah, also? . Specifically, if you can’t vote for someone who will make it better, at least vote for someone who won’t make it worse. Because it can always get worse.

From a conversation with a friend on a recent Facebook post. A memory of a memory, ghosts haunting the dusty rooms of my brain.

I once spent a very enjoyable afternoon in the of department library reading through century-old bound volumes of , which is now a somewhat obscure , but was in its day instrumental to the development of . All the great names were there—, , , et al.—and it was a clubby little world back then. Everybody who was anybody in statistics knew everybody else.

Just like today, they used a lot of space in their papers refuting each other’s papers. But the writing style was completely different, much more personal: many of the papers read more like conversations than the structured, pedantic language of modern journal articles in practically every field. “First I tried this, but it didn’t work, so next I …” “Like I said to so-and-so in a recent letter …” “According to whosit, such-and-such is true, but frankly, whosit is an idiot.”

Well, I recognized what they were doing: forming and having slow-motion . Everything old is new again. Sometimes I wonder if we wouldn’t be better off stripping out the modern pretense of detachment.

The “” death , like all cults, always . Most of the lies are stupid ones, but the cult does have some smart members, who know how to lie very well, and give each other cover. This is one example out of many. Always read with a critical eye.

Thiago Carvalho  
"When asked by Nature how the papers made it through review, a Sage spokesperson responded that the publisher relies on journal editors to make ind...
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