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ray__

1,027 karma · joined January 8, 2022

Consider the Kinder surprise egg, a quite astonishing commodity. The surprise of the Kinder Surprise egg is that this excessive object, the cause of your desire, is here materialized in the guise of an object, a plastic toy which fills in the inner void of the chocolate egg. The whole delicate balance is between these two dimensions. What you bought, the chocolate egg and the surplus, probably made in some Chinese gulag or whatever, the surplus that you get for free. I don’t think that the chocolate frame is here just to send you on a deeper voyage towards the inner treasure, what Plato calls the agalma, which makes you a wealthy person; which makes a commodity the desirable commodity. I think it’s the other way around. We should aim at the higher goal, the goal in the middle of an object precisely to be able to enjoy the surface. This is what is the anti-metaphysical lesson, which is difficult to accept.
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ray__··on First human injected with cancer-killing virus in clinical trial
A major difference is that no two breast cancers are the same. You're probably correct in your second point due to the sheer demand, but developing a treatment for any cancer is not the same as developing a treatment for an infectious disease because there is no one-size-fits-all strategy. A situation like the one you describe with simultaneous onset of breast cancer in a large population would definitely facilitate research and help lead to a better standard of care, though.
ray__··on Accelerated PyTorch Training on M1 Mac
What's your realm?
ray__··on Use fzf for tmux session switching
I see, thanks! This sort of use case would be rare for me, but when I've needed to manage sessions I've used screen. I can see how tmux would be valuable for managing more complicated groups of sessions like you describe.
ray__··on Use fzf for tmux session switching
I still don't quite understand the value of tmux, at least on a modern machine. If I need another terminal, I just pop open another terminal window and tile or tab it. If I want to keep a set of terminals organized, I use workspaces (at the OS level).

I can obviously see its value if there is no window manager or desktop environment on the system I'm using, but that's rare these days–if I'm working on a system with neither of these it's always over ssh. With a WM or DE it seems like tmux just adds a redundant layer of organization. What am I missing?

ray__··on Make Scientific Posters Easier Than Using PowerPoint
Agreed on the pricing, and IMO nothing can compare to a real vector graphics editor for posters (either Illustrator or Inkscape). How would you standardize fonts in figures or do true alignments with this tool (or PPT)?

BioRender is cool for premade vector images, but their license (and cost) is still too prohibitive for that, especially for grad students. Bioicons (https://bioicons.com) is a nice FOSS alternative.

ray__··on Sounding the alarm: How noise hurts the heart (2021)
Pro tip: one of the grey unlabeled buttons next to the screens on gas pumps mutes the audio. Muting those ads every time I pump gas feels like a subversive act in a dystopian Bladerunner-esqe society where ads are inescapable unless you know the hacks.
ray__··on The Uselessness of Phenylephrine
Opioid possession without a prescription is a class C felony
ray__··on The Uselessness of Phenylephrine
Interesting, thanks! I think I mostly took issue with the idea that throwing drug users in jail is the best course of action, and the condescending/judgemental tone of the original comment. I think we can dissuade substance use and abuse through other means (better drug education and rehabilitation, taxation, non-felony level criminalization) that will be a good middle ground between no drug laws and the draconian life-ruining ones that we have in place right now.
ray__··on Breaking PCBs for Science
Nice article, but that's a chinchilla! To be fair, way cuter than a mouse.
ray__··on Life advice from NYC chess hustlers
I love this, just subscribed. My favorite piece of advice:

“I’ll give you a lesson, a half hour for $20. I have some children that come just to see me once a week and I give them a lesson—$20 for a half hour. And there’s a lot of NYU students that come by, we give them a discount for being students. One hour for 40 bucks.”

ray__··on Mataroa blog – Naked blogging platform for minimalists
This is a huge factor for me. The best blogging/knowledge share/writing tools are the ones that have minimal overhead.
ray__··on The Uselessness of Phenylephrine
The fallout from the over-criminalization of opioids, meth, etc is a big reason that you're observing these behaviors. Stigmatizing drug use perpetuates the punitive approach to this problem. If the law treated addiction and the abuse of hard drugs with compassion rather than the draconian approach that we have in place currently you'd be seeing a lot less of this stuff.

This post could have easily been written about alcohol in the prohibition era. We've since learned that criminalizing alcohol makes its impact on society worse rather than better. We can't strip drug users of their autonomy and their ability to lead any sort of normal life and then act surprised when they turn to crime or turn back to drugs when they have nothing left.

ray__··on These are real compounds
The common names for compounds/compound classes like this are usually just left to the person that discovers them. The standardized naming scheme is set by the IUPAC and the name that you get for any reasonably complicated molecule will be a mouthful.
ray__··on Zotero 6
I assume you're talking about Papers? The main feature is that there's an iPad/Android app that syncs really cleanly.

With Zotero, syncing reliably across multiple devices was always hit or miss for me. Saving a few papers throughout my day, going home and reading/annotating them on my iPad, and then going back to work and pulling up a paper from the previous day with its annotations intact is the dream workflow for consuming academic lit that has always just worked with Papers but always required a lot of effort with Zotero. Maybe this is more of a "me" problem than a Zotero problem, but if I can't configure Zotero to sync reliably then many academics won't be able to.

There are some other neat features too. The built-in reader is good enough to not bother going with a third party. The handling of in-text references is better than any alternative (the actual reference is listed when hovering or clicking the reference number in text–a seemingly basic feature that lots of citation managers and PDF readers don't have that is essential for maintaining concentration). The handling of figures, metrics, and smart suggestion of related articles is also top-notch. I was sad to make the conversion from FOSS but haven't looked back yet. Hopefully this new Zotero release will make it possible to transition back–it looks like lots of killer features in Papers are offered by Zotero 6, which is great to see.

As for the rights-holding thing, most journals give their authors the right to distribute their work for free upon request, and there are some other loopholes for getting papers afaik, so I don't think it would be worth the time or effort to go after people with a few sci-hubbed papers in their Papers account. I am afraid that DRM will make this much harder though, especially for papers that have been downloaded on a university network for later offline reading.

ray__··on Ask HN: Single-person creations that have stood the test of time?
Richard Hollins Murray is somewhere in my ancestry (Murray is a family name), probably a very distant relative. God forbid someone mentions the cat's eye at a family party, though, because all of the great-aunts and great-uncles get up in arms about how Murray's idea was "stolen" and how Murray was the true inventor of the cat's eye. I don't think any of them really know the history (I didn't know his name was Richard before I saw his this post) but I'm not going to argue with a gang of riled-up octogenearians.
ray__··on The Unreasonable Math of Type 1 Diabetes
It isn't (entirely) genetic. There are some genes that are risk factors, but no one knows what causes T1D. It also doesn't affect you at birth–it's an autoimmune disease that usually manifests between the ages of 3 and 20 but can appear at any time in life (see the other commenter in this thread whose wife developed T1D in her 40s). In keeping with this, the risk factor genes are mostly related to the immune system. Even in populations with the highest risk haplotype, only ~5% develop T1D, and many people without this haplotype also develop T1D.

If it were purely genetic, evolution would have selected against these genes long ago since T1D was a terminal disease with a life expectancy of less than a year until the discovery and development of insulin-based therapies in the 1920s.

ray__··on Twitter misses ad revenue and user growth estimates
I never understood Twitter until I started using it professionally, if you could call it that, as an academic. "Science Twitter" complements traditional academic publishing models really well. When I want updates about science, I read papers that I find from searching, RSS updates, or citations. When I want updates about _how science is done_, I turn to Twitter, where many of my scientific role models are active and almost all of the interesting stuff tends to bubble to the top.

Its algorithm seems to work really well for rapid consumption of buzz within a particular network that you can tap into by following people. It is one of the few cases where I like the fact that I occasionally get out-of-network Tweets in my timeline because it usually exposes me to something really interesting posted by someone outside of my direct field. I'd never want to use Twitter for comprehensive reviews of some topic, reliable back-and-forth discussion, etc. but it's just fantastic for gossip and trends.

The tables here are even starting to turn–so many people are on Science Twitter that it feels like I find as many new and relevant papers on Twitter as I do in my tailored email notifications and RSS feeds. Twitter is also always a day or two ahead, and the papers usually come with the backstory and context in plain English. I hate to say that the Twitter thread from the paper author is often more informative (at least, per unit of time that it takes to consume) than the content of the paper itself.

ray__··on Last-resort cancer therapy holds back disease for more than a decade
Vasculature in and especially around tumors is usually different. Malignant cells consume a vast amount of energy relatively speaking, and often over-express proteins that recruit blood vessels in order to feed this energy demand (VEGF is the one that is discussed the most afaik; this process is called angiogenesis). Inhibiting these proteins is a common chemotherapeutic strategy, see bevacizumab and ranibizumab. Despite this process most solid tumors are hypoxic at their centers and hypoxia-activated prodrugs that are "activated" within hypoxic environments (and toxic after activation) is yet another chemotherapeutic strategy, see evofosfamide or apaziquione.

Solid tumor penetration isn't really related to this though, it has a lot more to do with the fact that it is physically difficult for a molecule to diffuse through the many layers of cells that make up a solid tumor. When you take a drug, it generally ends up in your bloodstream and from there must diffuse through the lipid bilayers that encapsulate cells (whether they be cancer cells or not) in order to reach their target. This diffusion is a big barrier when it comes to designing drugs, because most things won't passively diffuse through lipid bilayers. A successful small-molecule drug will be able to 1) bind to its target effectively enough to stop that target from doing some disease-causing thing, 2) not bind to other things that are important for cellular function, and 3) get into the cell in the first place, without being broken down before it gets there. Balancing all 3 of these requirements is tricky, but rules of thumb have been developed for 3) that help guide the design of small molecules.

Perhaps the most important guideline for 3) is size. Most small molecule drugs (anything that you take in a pill, along with many chemotherapeutics) are designed to be < 500 Dalton. Once you get over 800-1000 Da diffusive cell penetration is rare (there are interesting outliers, cyclosporine cruises through lipid bilayers despite weighing in at ~1200 Da). Immunotherapy generally involves retraining your immune system by introducing antibodies (~150 kDa+) or whole T-cells. These modalities can generally only target things on the outside of cells, because there is no way they're getting inside, and they certainly won't be able to pass through the many layers of cells that make up a solid tumor.

tl;dr is that immunotherapeutic agents won't be able to penetrate solid tumors by diffusion because they (the antibodies and cells involved in immunotherapy) are too big, and there isn't any other mode of entry. I do wonder if a true immune response would need to penetrate at all though, because presumably T-cells would break down a solid tumor layer by layer if the appropriate antigen was present. I'm not sure how correct this line of thinking is though.

ray__··on Google Research: Themes from 2021 and Beyond
I'm surprised that there was no mention of AlphaFold2.
ray__··on Radeon RX 6500 XT is bad at cryptocurrency mining on purpose, AMD says
I started using Nvidia cards with Linux about two years ago and haven't had a single issue so far. It has always been Ubuntu, so that might be part of it, but I get the impression that Nvidia's beef with Linux isn't an issue anymore.
ray__··on Systemd, 10 years later (2020)
"I found the description very descriptive" - an idempotent system in action.
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