🏒 Fun to see a winning team at this venue, for once, and with a massive amount of goals. Will come back.
When I wrote that opening up science and increasing trust in it are mutually opposed goals, I didn’t imagine the perfect example would come up so soon in both the thing that happened and the commentary about the thing. It is helpful, when interpreting what follows, to keep in mind CS Lewis’s lecture on The Inner Ring with the following two adjustments: there are in fact many rings, concentric, with people ordered in them according to some gradient; and although academia has the secret rings Lewis talks about there are also many public ones with members known, where the innermost ring to a high degree overlaps with Harvard.
The first thing that happened was a segment on 60 Minutes, America’s premier newstainment show, about the current administration’s defunding of Harvard and the implications for science. A few scientists gave interviews, including a bench researcher whose lab studied “different aspects of cancer biology, including tumor heterogeneity, cell-cell interactions, tumor microenvironment, cancer metabolism, drug resistance, and cell signaling.” So, very much a “cancer researcher”, though as far removed from the practical aspects of cancer management as you can imagine. Still, from applying for grants to writing up research results for peer-reviewed journals, scientists have been conditioned to tie whatever they are doing to real-life, practical applications: in the interview Dr Brugge said what she and her post-docs must have written hundreds of times before, that her work has the potential to prevent breast cancer.
There is a legitimate discussion to be had about overblown claims to practicality. The debate has in fact been ongoing for decades now in the editorial pages of various scientific journals. But then someone formerly of Harvard, then Duke, then out of academia completely after a legal dispute, wrote about the issue in light of the segment. This is the second thing that happened.
The article for the most part lists personal observations about the two scientists interviewed for the segment (the second was David Liu, about whom the authors had kinder words). It very much had the sound of someone expelled from the circle grinding an ax with the inner ring. This led to even its salient observations being framed somewhat maliciously. For example:
Universities and their faculty have learned that success in today’s system depends not as much on actually doing science but on marketing the perception of science — framing even routine findings as lifesaving advances. “Cancer” has become a brand, a universal justification for more funding and prestige. The public sees heroism; insiders see dollar signs. One of the strangest features of this ecosystem is how many researchers who do pure basic science — work with no foreseeable medical application — nevertheless frame their research as “curing cancer.”
Which goes from pure speculation to undisputable fact. The need to frame everything as “curing cancer” stems from all the money being allocated to cancer research. It is all about the incentives: Willie Sutton robbed banks because “that’s where the money was” and scientists are no different.
But did I just, even in this gentler framing, compare scientists to bank robbers? See, this is why the debate is best held behind closed doors, lest a politician uses the fact that most research findings are false as an excuse to cut funding. This is what most comments to [Mike
This is the open science dilemma: have the debate out in the open and risk providing ammunition to your enemies? Or do it behind closed doors and risk mistrust? A few decades ago the point was moot as the “enemies” were first powerless hippies, then only slightly more empowered religious zealots. As we all know, the anti-science front has since strengthen. Why that is, well, that is yet another debate. Since one of the reasons is that many scientists openly picked sides, whether out of conviction or out of fear from being ostracized, this is also a debate best held behind closed doors.
Until that happens, we will continue to have dialogues such as this one, The link is to what I think is the final post in the back-and-forth, which I think is the only guaranteed way to show the entire thread, but X truly wasn’t built for sharing these kinds of interactions and is not the best medium for having them. all in support of the beef-industrial complex. Other fields have already wised up: the Internet is dying on the outside but growing on the inside, with important conversations moving to private forums. Which, as I argued, they should.
After citing Niko McCarty’s list of 30 biomedical essays yesterday, I had an urge to find each and have a separate post linking to them. Well, good thing I procrastinated because he just came out with an ever longer list (130 and counting) that does have the links. Still no Mansions of straw…, but I’ve just asked asked him to consider adding it so let’s see how the list evolves.
You may have noticed more linked lists on this blog, starting this summer and ever-increasing. This is the direct result of moving my RSS reading from (mostly) NetNewsWire on the phone to (mostly) Feedly on the Daylight tablet. Whatever the cons I thought it had in the beginning, they melted away as the proof is in the output. Interestingly, I hardly ever use the pen, but did pair it with an old (pre-Touch ID) Magic keyboard encased in this handy case/tablet stand and this light-weight pair of devices is all I need on most short trips.
Now, it is not a cheap device! There is currently a 48 hour pre-Black Friday flash sale, and it is still $649 pre-tax. It is also much less versatile than an iPad (no camera and therefore no video calls, and certainly not a good media player although being an Android tablet it does have an official YouTube app, unlike some other better-screened devices. But if you already have a large phone and a laptop, does that middle screen truly need to be a full laptop replacement?
I was also pleasantly surprised by the (heavily customized) Android tablet interface. Things have evolved quite a bit since I briefly owned a Fire tablet, which appropriate to the name I wanted to burn in an effigy. I haven’t owned a Remarkable or a similar e-ink device, but from the refresh rate alone I would guess my reaction would be the same. The plain old LCD technology that Daylight uses Even though, yes, they’ve rebranded it to “e-paper” and say it’s their invention. I don’t know enough about screen technology to comment on whether this is valid, but to me it smells like mostly marketing. was the perfect compromise for my uses, and one I hope more companies would emulate.
🏒 Fun to see a winning team at this venue, for once, and with a massive amount of goals. Will come back.
📺 Common Side Effects (2025) worked for me on at least three levels: as a Mike Judge satire (and I love Mike Judge), as the spiritual successor to Scavengers Reign (ditto), and as a true-in-spirit if not in fact look at the American pharmaceutical industry (and here I could link to half of this blog). With 10 episodes of about 20 minutes each — the runtime of approximately one Irishman — it is well worth seeing at a single go.
A brief update to yesterday’s post notes that there are still people who care about the true meaning of epigenetics, and even call themselves theoretical biologists. Note that the Institute for Systems Biology is not some drive-by operation, and indeed is the home of this year’s winner of the Nobel prize in medicine. There may be hope yet. (ᔥJeffrey West, on X)
I did it: I have found my coffee preciousness threshold. Our local coffee shop changed suppliers and only had the beans depicted below to offer. The very helpful barista even offered to pack me a bag of their own in-house coffee beans, which I declined but should have taken as the warning it was.
Because the beans were… fine. For a light roast, and particularly for the price. Perhaps even on par with Bird Rock, though I will need to make more than one pot for a real test. But everything about this coffee was over-designed, from the embossed packaging to the transparent plastic bag holding the beans to the “tasting notes” insert tucked into the outside pocket. And just look at that website (and the price)!
I am in fact embarrassed for buying it. Who is this for, and do they also own a Juicero? I choose beer over wine because I am repelled by the (usually faux) sophistication of the wine connoisseurs. I’d better reign in my coffee enthusiasm or else switch to tea.
People are not rebelling against economic elites, but rather against cognitive elites. Narrowly construed, it is a rebellion against executive function. More generally, it is a rebellion against modern society, which requires the ceaseless exercise of cognitive inhibition and control, in order to evade exploitation, marginalization, addiction, and stigma. Elites have basically rigged all of society so that, increasingly, one must deploy the cognitive skills possessed by elites to successfully navigate the social world.
As a card-carrying member of the cognitive elite, I fully support the rebellion.
I have been using OmniFocus since 2016 and from the very beginning have kept a running list of blog post ideas which I almost never use. “Write about Taleb’s VC quote” says an entry from October 11, 2024. More than a year later I did write about it, but not because I saw it on the list and have in fact only just now realized that it was on the list in the first place. The oldest active entry is from August 15, 2021: “Write about theoretical biology”. The second-oldest is from four days later: “Write about Waddington’s epigenetics”. This was a few months before I had read any of his books, so maybe it was just mine discovering what Waddington did? In any case, consider this post as a way to cross both of these tasks off the list.
And yet again, the writing is not prompted by any list, but rather by this question on X — what are the major breakthroughs in biology that were idea-driven arguments based on existing data — which duly reminded me of CH Waddington (or, as iOS 26 autocorrect misspelled it just before I had hit return, “CH Washington”). Waddington, a proponent of theoretical biology as a parallel to theoretical physics, organized symposia in the late 1960s on the topic. Alas, it never took off. He died in 1975, age 69, just in time to see research funding for experimental biology skyrocket making everyone an experimental biologist. The theoretical part is now mostly mathematics: see, for example, the Mathematical Oncology newsletter, but what Waddington proposed was not really maths. Interestingly enough the man behind the newsletter, Jeffrey West, has co-authored a paper with Taleb that was very Waddingtonian, with a recent follow-up and a whole book (which I am yet to read).
For an example of what Waddington wrote about see his most well-known work: the epigenetic landscape, proposed before we even knew what genes were. To me these were incredibly useful when thinking about differentiation of complex cells and how it can go sideways. It is also incredibly annoying that the term epigenetic has been hijacked by molecular biologists to mean solely chemical changes to DNA and adjacent proteins which are more likely than not merely a sideshow to what really controls gene expression (3d structure, mRNA, other genes, i.e. everything that goes into a gene regulatory network). Ask a doctor what epigenetics means and the first thing they say will be acetylation and methylation, and if they are oncologists they will talk about “epigenetic drugs” whose job is to inhibit methylation (“hypomethilators”), or what not. I would wager that GLP1 inhibitors like Ozempic are more epigenetic than the most active hypomethilator, but I may as well go after windmills.
Now, the person who asked the question that kickstarted this thinking is the founding editor of Assimov Press which is a charming publication about science and scientific progress. I hope his asking questions will lead to more writing about what happened to theoretical biology and that I’ll learn more about people who carried the flame (or, more likely, rediscovered the concept after everyone forgot about poor old Waddington).
Update: Dr. West has pointed me to the work pf Sui Huang from the Institute for Systems Biology who has tried to bring to terms the two different meanings of epigeneticts with explicit tie in to GRNs. I am sure that very paper is where I got the notion from, but have of course completely forgotten about it. Thank you, Jeff!