Posts in: science

For Valentine’s Day, The Washington Post decided to write about a promising new male contraceptive drug being studied in mice. That’s fine. What’s unusual, bizarre, and a bit of a troll is hanging a red banner over the front page presenting it as breaking news. Seriously, WaPo?

When Russ Roberts, my favorite interviewer, speaks with Adam Mastroianni, the author of my favorite newsletter, of course I have to share it. No excerpts, just listen to the whole thing, please.

The academic prisoners' dilemma

As of this year, eLife no longer has “accept/reject” decisions after peer review: Which I learned via Andrew Gelman.

All papers that have been peer-reviewed will be published on the eLife website as Reviewed Preprints, accompanied by:

Authors will then receive a paper with a full DOI that can be used on funding applications. They will be able to include a response to the assessment and reviews, and decide what to do next:

  • Revise and resubmit
  • Declare the Reviewed Preprint as the final Version of Record

This is as it should be in the age of unlimited digital space.

The quality of public peer review on eLife seems above average: I have once, as the sole peer review of this paper from a double-digit impact factor journal, Impact factor of eLife, per Wikipedia, is 8.7 received a single sentence which amounted to “sample size too small”, but with more spelling errors and the same lack of punctuation. If your goal when reading a paper is both critical appraisal and learning, you could do worse than reading this exchange.

But! Eleven reviewed preprints total in the last 5 months seems… low? Am I missing other public reviews? I would, for example, very much like to learn what the reviewers said about this.

More generally, I am worried that this will make eLife become the default publication of last resort — trouble for the Infection and Immunity and Leukemia and Lymphomas of the world, but not exactly the killing blow to Science or Nature or most of its million offshoots.

The current, bizarre, inefficient, unsustainable — Byzantine, if you will, thought that is too disrespectful of Byzantium — keeps itself alive through force of reputation. Critical thinking is hard, so unless I am in the opposing team and my goal is to tear down your data I will save many a mental cycle by “trusting the process” and taking the conclusion, abstract, that one piece of information I need to cite in my own work… at face value. And evidence to the contrary be damned, say published in NEJM to a clinician and their ears will perk up.

So we are in a prisoner’s dilemma of sorts. Take a group of one hundred researchers: the average benefit to all of them, and to science in general, would be greater if all published in eLife. But, if 90 of the 100 submit to CNS journals or NEJM first then go down the impact factor list and only 10 shmucks go straight to eLife, there will be only a handful of “winners”, the state of science remains what it is, and everyone ends up wasting so… much… time.

It doesn’t have to be this way – and Covid did expedite some reputational decay – so this is a good a time as any to place a chisel in the crack. What’s needed now is some forceful movement of the hammer and, well, I guess people who publish People who review are equally important, but maybe just maybe we will at one point be able to leave that to an algorithm. It would certainly do a better job than most! are the hammer in this strained analogy.

Should I start with myself? I do have a handful of side projects which are neither industry nor strictly academic — myself having no academic affiliation. Stay tuned.

February lectures of note

NIH has always made most of its lectures available to public. With the pandemic, the production values have gotten better, and more people have gotten used to viewing lectures online. Here are a few interesting ones scheduled for this month. Some of them are part of NIH’s Demystifying Medicine series which is open to public and tries to target the curious layperson Alas, not always successfully. to the best of presenters' abilities.

Fact Stranger than Fiction: Adventures in the Genomics of Inflammation

Somatic Mutations in “Benign” Diseases

  • Speaker: Neal Young, MD
  • Date: Tuesday, February 14, 2023, 3:00 - 4:00 p.m. ET
  • Register here.

The Use of JAK Inhibitors in Autoimmune Disease

Clinical Center Grand Rounds: How Nucleic Acid Structure and Chromatin Environment Influence Gene Transcription

Nitpick of the day: clinical trial versus clinical study

At the very start of the textbook Fundamentals of Clinical Trials the authors make a distinction between clinical trials — comparing two or more different interventions — and clinical studies, which merely describe an intervention without comparing it to anything. So, there can be no such thing as a “Phase 1 trial”, since they typically involve a single drug at different doses and schedules. The only true trials, according to the authors, would fall under Phase 3, or Phase 2b at the earliest.

This is stupid, misleading, and not at all how the words “trial” and “study” are used by anyone else, including the biggest and most important drug regulatory agency in the world. There are many such pointless exercises of professorial power in medicine, including my favorite: whether the correct pronunciation of “+” in “7+3” is “plus” or “and”. They amount to nothing more than purity tests that award the wielders of the right language a false sense of precision. As Nassim Taleb wrote, nitpicking is the enemy of thought.

The rest of the book is good enough, but more on that later.

National Cancer Advisory Board meeting on February 9

The National Cancer Advisory Board is as big of a deal as it sounds, but have a look at their Charter — Description of Duties in particular — and try not to yawn. I suspect whoever wrote this also writes grant application instructions. May this in part be why science is bogged down?

In any case, the Board meetings are open to public. The next one is on February 9, 2023 at 1:15pm EST and can be viewed at videocast.nih.gov. That website is itself a trove of excellent recordings unrelated to federal body deliberations: just last week there was a lecture on bacterial immune systems, here is my old boss talking about interleukin-15, and hey what’s this?

Science and medicine blogs on FeedLand

After a few months of intermittently kicking the tires on Dave Winer’s FeedLand, I’ve finally had the time to port over a few feeds from my preferred RSS reader. The wonderful thing about FeedLand is that you can easily follow my feed categories and read posts without having an account (which is fortunate, since new signups on Winer’s own server are on hold). The full list of feeds is here. There is even a feed of posts I liked! It’s feeds all the way down.

The Science category has your usual suspects but I had to dig deep for Medicine since many of the blogs I follow haven’t been updated in years and others have turned into HuffPost-level text mills. Fortunately, Substack enabled a resurgence of medical writing, with feeds enabled by default.

Did I mention NetNewsWire is a free, open source RSS reader available on MacOS and iOS, and can sync via iCloud? For the anti-Apple readers, Feedly is there, I guess?

This April will be 10 years since Elsevier aquired Mendeley, up until then the best reference manager around. And it took longer than expected, but it looks like they finally killed it.

To all the Mendeley refugees: Endnote is just as bad, and in many ways worse. Get Zotero.

Invention versus discovery, medical treatment edition

Google Scholar alerts are a quick if crude way to be up-to-date with literature. In addition to journal articles and conference abstracts it also looks at U.S. patent applications, and despite the impenetrable legalese something will ocasionally turn up that is at least amusing, if not informative.

Today was one such occasion: a patent for a combination of two already approved drugs to treat toxicity of CAR T-cell therapy, by the group which, admittedly, was the first to give CAR T-cells to humans and the first to treat their side effects.

I may be showing my ignorance of U.S. patent law here but, how is this a thing? These drugs are already commercially available and widely used for exactly this indication. How would they enforce this patent, and how exactly would the patent help with development and commercialization of two drugs which are already on the market?

After reading Steven Johnson’s Where Good Ideas Come From I realized that not everyone makes the distinction between discoveries and inventions, Which is the first website that DuckDuckGo returned, and it is servicable, but I was flabergasted by the long list of nearly identical websites with domain names all some variant of “difference between”. This is how ChatGPT destroys Google. and this may be an example of a discovery masquerading as an invention. Nothing was created — the drugs were already there — the team merely discovered that those two drugs work in a specific indication. If this is deserving of a patent, should every drug combination be patented?

To be clear, I am not a lawyer — caveat lector — but the whole patent system needs an overhaul and making a clearer distinction between discoveries and inventions should be one of the items on the long list of things that need attention.

A lengthy overview of the implications of ML/AI to biology and drug discovery came out yesterday, and while I appreciate its enthusiasm and breadth, the answer to the question posed in the summary — What if this time is different? — is, sadly, no, probably not.