Posts in: science

The Good Science Project is underselling how good it is. More like this, please. (signatures below the manifesto are a good — heh — example of quality over quantity)

🧪 Good morning to everyone except to whomever is in charge of the eRA Commons service desk. You’d think that a multi-billion dollar operation like NIH would have a decent answering service, with a call-back option, number in line, etc. ★☆☆☆☆, won’t use again (if only)

A marvelous xkcd from a few days ago. This one strip explains the trouble with odds ratios better than hours of premed/med stats 🧪

Science and scientism

A big reason Don’t Look Up didn’t sit right with me was its simplistic view of the scientific consensus. “Listen to the goddamn qualified scientists…” bellows Ariana Grande paternalistically.

Meanwhile, qualified scientists from reputable institutions of higher education act as petty and vindictive prima donnas. The linked article is one scientist’s story of having to suffer through years of academic harassment for publishing a paper that rubbed some of her fellow researchers the wrong way. From the abstract:

A naïve researcher published a scientific article in a respectable journal. She thought her article was straightforward and defensible. It used only publicly available data, and her findings were consistent with much of the literature on the topic. Her coauthors included two distinguished statisticians. To her surprise her publication was met with unusual attacks from some unexpected sources within the research community. These attacks were by and large not pursued through normal channels of scientific discussion. Her research became the target of an aggressive campaign that included insults, errors, misinformation, social media posts, behind-the-scenes gossip and maneuvers, and complaints to her employer. The goal appeared to be to undermine and discredit her work.

Goddamn scientists indeed.

Godwin’s Law and the Rise of Hyperbole on MedTwitter

Saurabh Jha:

“Today’s Galileos fight over one or two vaccine doses in teenagers, whether the risk of vaccine-induced myocarditis is 1/1000 or 1/10, 000. Nothing encapsulates our pettiness more completely than our probability wars.”

Echoes of Chris Hitchens here.

A brief chronology of my employment

  • 1994: Fifth grade; I am charged with editing the school newspaper. There is an Intel 386 PC at home that is about to be upgraded to a 486 and do something more than run Lands of Lore.
  • 1996: Seventh grade; I typeset a book of poems1. The school newspaper becomes the school magazine — in layout only; the publishing schedule remains haphazard — as I upgrade from Word 6.0 to QuarkXPress
  • 2000: High school starts again after a freshman year interrupted by NATO bombing. I make the town library’s official website. It is a php hack job laid out in tables instead of the newfangled and to me unknown CSS; it still wins an award.
  • 2002-2008: Med school; I typeset a book here and there and occasionally help out with the library website.
  • 2009: Teaching assistant, Institute for histology and embryology, Belgrade School of Medicine.
  • 2010: Resident, Internal medicine, JHU/Sinai, Baltimore MD.
  • 2013: Chief resident, Internal medicine, as above; I understand the benefits of not being invited to a meeting.
  • 2014: Clinical fellow, hematology/oncology, National Cancer Institute, Bethesda MD.
  • 2016: As above, but also Chief fellow ex tempore for the joint NCI/NHLBI fellowship; my hatred of poorly-run meetings intensifies.
  • 2017: Staff clinician, later to be renamed Assistant research physician, Clinical Trials Team, Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda MD; the 1994 me marvels at the word salad trailing the title.
  • 2021: Chief Medical Officer, Cartesian Therapeutics.

  1. Someone else’s, to be clear. ↩︎

Blogroll

I, for one, am glad that blogs are making a comeback. Here are a few I’ve been reading for at least a few months, many of them for years, some for decades.

Applied philosophers

The only true philosophers of our time.

The new scientists

People without major academic credentials who have interesting ideas about science.

The old scientists

People with major academic credentials and interesting ideas, something to teach, or both.

The ludites

People against modernity of one sort or another.

People doing their own thing

Unclassifiable but exhilarating.

Apple enthusiasts

Some tips, a few tricks, many opinions.

Finance-adjacent

Economists and investors, for the most part.

Journalist-cum-substackers

Former or current journalists who now earn some or all of their living by writing newsletters via Substack, which is slowly reinventing blogs (in the sense of reinventing the wheel, not actually making them better and in fact in many was making them much worse).

Company blogs

For when I really want to know when the next update is coming.

Clearing the PDF log jam

There is a crisis in medicine, but not the one you think: And not only in medicine, of course.

Reading primary literature is superior to press releases and tweets — it sounds so obvious, but not many physicians act on it. There no prizes to be won for not just following the KOLs[^kol], Key Opinion Leaders, the influencers of medicine before influencer became a real noun. Note that unlike the influencers of social media KOLs don’t use the #sponsored hashtag, though there is a hashtag equivalent. nor do you save any time. Quite the opposite: instead of a promoted tweet about the me-too drug de jour falling into your lap, you need to find a way to identify what’s worth your time reading, and also find time to actually read it — not a small achievement, as highlighted by the above tweets.

But then what? Sure, there is profit at the end of the rainbow in the form of useful knowledge, but merely reading a PDF may not result in any knowledge at all, let alone knowledge you can use. Or, as the [underpants gnomes][gnomes] would put it:

Underpants gnome meme with the text Phase 1: Read PDFs, Phase 2: ?, Phase 3: Profit

I too had a backlog of unread PDFs once, spent so much time organizing files and folders, using this and that program to store the metadata, NB: if you write any sort of scholarly texts you will still need a reference manager, no matter what system of organizing PDFs themselves you choose. I recommend Zotero, lest your institution has a requirement for Endnote (which must have quite a salesforce, to so thoroughly insert their buggy, laggy, slob of a program into every academic crevice). trying out plain paper, a Kindle, an iPad or two, thinking it is how I was reading them that mattered and oh if only I could find the perfect setting, under the shade of an old oak tree perhaps, with some peace and quiet, a pen in one hand and a cup of coffe in the other, well, then the unread pile would melt away and all would be good in the world.

But reading is easy, if what you read is useful, entertaining, or both. For most people without visual impairments or dyslexia, the log jam is at Step 2. We don’t want to read our pile of PDFs because, in most post-GME circumstances, there isn’t a clear goal to reading them (lest you have superhuman memory). The clear exception here being board exam and MOC prep, where the goal is obvious and the sources of information are all spelled out. This is particularly true early on in your carreer, when you have nothing to hang your hat on mentally, and few connections to make between what you are reading and what you already know. Sure, you don’t need to keep track of the articles you’ve read if the only reason for reading is to pan them on Twitter. You do, however, want to summarize what you’ve read and save it for future use, be it in a lecture, article, grant proposal or a blog post. So if and when you find a fairly obscure but potentially important fact about this or that cellular pathway in a supplemental figure from a CNS-adjacent journal, and you memorize the fact for later use, and then a year or so later you do use it to make a figure for the background section of a clinical trial protocol, well, what you do not want happening in that case is to spend hours of your life trying to retrace your steps and figure out the original source when a fellow Yes, this has happened to me. We do have good fellows. asks where you got the data.

I wouldn’t be admitting to all that if I didn’t think I’ve found a solution. A few years ago, I replaced the unsustainable routine of just-in-time literature reviews for whatever I needed done with a robust knowledge management system — a GTD® © David Allen Co. 2001. It is a good system though. for ideas, if you will. It got to a point where I can read at least one article every day and skim a few more, get the useful information out and into my app of choice The app of choice before DEVONthink was Roam, which is a web service and a marvelous one at that, but unfortunately not much into encryption, privacy, and other things people dealing with confidential information like to have in the tools they use., and have all the information I need to write an editorial like this in a morning or two.

As with most of the things I do it is too personal and Rube Goldberg-y to be of use to anyone else, but it started with a forum post and a book, and if you’d like to turn your plate full of PDFs into something more usable may I recommend that you start with one or both of those and see how it goes. Could it be any worse than what you’re doing now?

What I believe that most people probably don’t (no data behind this, just the armchair)

The world in general, and the US in particular, is spending too much on goal-directed, targeted biomedical research while undervaluing both applied and theoretical physics. Picture Leonardo da Vinci drawing helicopters: that’s the modern-day cancer researcher. The universal cure for cancer — and there should be one, if humanity survives long enough to create it — will not come from an NIH grant. If grants are involved at all, it will be something initially funded by the National Science Foundation. The current system of funding (government, non-profit, biotech, you name it) is broken, and if you account for the opportunity cost it is a complete disaster. Each of these statements deserves at least a paragraph, but I am saving my carpal tunnels for a manuscript, an LOI, and a couple of protocols (oh, the irony).

In the meantime, a few things physician-scientists should do for the overall good:

  • find causes and create better prevention strategies, because a look at the SEER database will tell you that it’s not just bad luck;
  • eliminate barriers for administration of known curative therapies world-wide (do we really want to leave this to politicians and economists?);
  • ensure rapid and honest evaluation of the many new treatments, procedures, and diagnostic/prognostic methods coming out of the biomedical behemoth.

How beneficial any of this would be for one’s career is a different question altogether, but let’s not get into incentives because RSI. I am also very open to opposing opinions, since my being wrong would make my life easier.

Storytellers

Last week I shared a brief reflection on a tiny aspect of my commute. Please check it out it if you haven’t already, it is a quick read.

Wasn’t that nice? It started by introducing some old concepts in a new light—you knew about trains before, and maybe even knew there was a MARC Penn that line goes from Baltimore to DC, but probably didn’t know the specific trains and their timetables. Then it gave you a coherent explanation of a phenomenon you hadn’t known about before. This first caused slight, but not unpleasant, cognitive strain while you were figuring out what I writing about, followed by the small pleasure of an ah-hah moment once the pieces clicked.

It was a brain massage, if you will. It was also complete bull.

Not that anything I wrote was wrong, as far as I know, but I didn’t give many arguments for it being right, either. There were no ridership statistics or arrival times to back up my claims. And even if there were—I didn’t give any alternative hypotheses to explain the situation, nor reasons why those would be less likely than my own explanation. When you think about it, it was more of a brain Twinkie than a massage—all empty calories, with a fleeting feeling of fullness.

Welcome to 99.99999% of the written word, and to anything ever spoken out loud.

We like stories. They need to make a threshold amount of sense (this is why societies universally ostracize schizophrenics). They should contain an element of surprise (it is not that the 7:07 train would come later than the 7:23—twists like that do not surprise anyone any more—it is that it comes in much earlier because people think it wouldn’t). And they get bonus points if—as my last parenthetical implied—they paint the others as stupid or incompetent. There are many more checkboxes; more of them checked, the better the story.

Most professions are based on storytelling. Doctors tell different stories to their patients, each other, and themselves—as do most other scientists, to a different degree. Lawyers tell stories to their clients to make them believe they will craft good ones for the judge, jury, and the opposing side. Ask a marketer what makes a good commercial (spoiler: story).

Being a coal miner doesn’t involve telling stories. No one wants to be a coal miner.

Our minds prefer a good story over a true one, and will have us believe it more, too. However, the more boxes you see checked, the more suspicious you should be that someone manipulated the tale to make it more pleasurable, ergo memorable, ergo believable.

(So, if what you’ve just read made sense…)

If you are looking for an objective truth—or getting as close to it as possible—any medium that involves audio/visual queues will be an impediment. Sights and sounds stir up emotions, and emotions prime us to believe or not to believe. Pay attention to the background music in a documentary, or how the desk of that shifty lawyer they’re interviewing is a complete mess.

TV news is, of course, a joke—this is why comedy shows are becoming the most popular delivery form.

Written word has its own way of deceiving—anecdotes, incomplete data, misquotes, lazy references—all to make a better narrative. Just read anything by Malcolm Gladwell. And look at the time it takes to get to the bottom of just one tiny factoid in that story of the iron content in spinach. Finding truth is exhausting and exasperating, and people whose job it is to find it (hello, accountants) are way less fun than those who make stuff up. Mark Twain said it best:

A lie can travel half way around the world while the truth is putting on its shoes.

Misquoted? Most likely. Or is Huff Post wrong? It wouldn’t be the first time.

There is nothing in this post that bigger and better minds than my own haven’t written about already. But that’s a boatload of pages! Not many people have the time, discipline, and interest to read all that—and even if they did, they would keep making the same mistakes over again, as shown in several studies described in those same books (yes, yes, all studies are flawed; one windmill at a time, please). These things are hard-wired, and for a good reason—evolution doesn’t care for objective truths.

Or maybe it does. I don’t know, I’ve just made it up.