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murphyslab

875 karma · joined August 22, 2017

Scientist. Chemistry and Nano/Materials
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murphyslab··on Unusual Suspects
I wasn't aware that the number of cases was so small that it might spoil for others. I see now, trying it on a desktop, that there are just 68 cases at present; there isn't an indication of that on the mobile version.

Moreover, I cannot edit my previous comment.

murphyslab··on Unusual Suspects
That was incredibly fun, although challenging on a smartphone. If you can guess the character it's a lot easier (100%, 99%, 96%, 85%), but even with ones I couldn't guess, it gave a reasonable score (Hollow Knight: 74%, Steve Harvey: 84%, Sirenhead: 69%) for following the directions.
murphyslab··on AI in drug discovery – what it is, where we stand and the path forward
NB: The post was updated twice. The first changed the link to the Nature Reviews Drug Discovery article; the second changed it back to Derek Lowe's blog post with the NRDD article in the body.
murphyslab··on AI in drug discovery – what it is, where we stand and the path forward
My apologies for the lack of clarity in my prior comment; it was composed in haste. To be clear, I am a bit of a Derek Lowe fanboy. I value the work that he does in offering insight on his areas of expertise to the public at large because he has both the necessary understanding and the ability to communicate clearly. Few people have his level of background knowledge alongside the capacity to wade into the depths of pharmaceutical chemistry and then communicate that information and his personal perspective to enrich the commons.

What I was getting at with the issue of credibility is that I (or most others) would have time determining if a particular scholarly author in pharma is a good person to listen to on the subject. But having evidence that Derek Lowe is an honest broker of information in that domain, given his long history of commentary as well as other chemists I know who eagerly read his commentary, I'm willing to defer to his assessment.

murphyslab··on AI in drug discovery – what it is, where we stand and the path forward
Derek Lowe is someone whom I greatly admire and his work as a science communicator is a true service to the profession and to science at large. It is not intended as an insult in any way. I've known a great number of competent chemists, but few are as effective as communicators as he is.
murphyslab··on AI in drug discovery – what it is, where we stand and the path forward
Derek Lowe as a science communicator, and others like him, is sorely needed to understand the real meaning and significance of the study and others. I say that as someone with a PhD in chemistry who's been to plenty of presentations on drug discovery topics.

It's difficult to calibrate statements made by other scientists unless you're well embedded within a field: Is this someone whose opinions matter? Are they the subject matter expert they make themselves out to be? Is this research itself truly impactful? Is it really 5 years until it will be realized outside of academic labs? Etc...

It's difficult to decipher questions around credibility because they rely on real-world interactions and associations that extend beyond the physical tokens of paper counts, publication venues, citations, and author lists that typically lag behind the front of human knowledge which is generated from real-world interactions. It can be simple things, like the insightful question a grad student, with minimal publication history, asks in a seminar.

Of course, the paywall is also unhelpful too, but a good, brief commentary by an appropriate commentator is a better link for 99% of prospective readers compared to most "peer reviewed" (scare quotes because that's a real question nowadays) articles.

murphyslab··on Show HN: Isopolis – Isometric pixel map of SF
Men in Black: https://floor796.com/#b2r4,541,605

Naruto: https://floor796.com/#t2l4,684,675

The author continues adding and refining the project, so if it isn't in there yet, perhaps in the future.

murphyslab··on Show HN: Isopolis – Isometric pixel map of SF
Incredible. It's easy to just go on browsing and exploring. The massive, scrollable pixel art aspect reminds me a little of Floor796: https://floor796.com/
murphyslab··on Show HN: CheapFoodMap – A map of good meals under $10
Noticing all of the Costco hot dog listings on the map reminds me: There's also an incentive for businesses to pose as users and misreport prices of competitors. My local Costco gas station constantly has a set of users misreporting the price of fuel, reporting the price as several cents higher than in actuality, seemingly in order to prevent consumers from refueling there. Something to watch out for.
murphyslab··on Amid nurse shortage, a university rolls out the welcome mat for men
> I was aggressively recruited for education as a math undergrad.

Was it because you were male or because you were studying math? Many schools struggle to find good math teachers; it's one of the qualifications in perpetual shortage.

murphyslab··on Show HN: 18 Words
Suggestion: Require a user to hit ENTER or SPACE to clear the word, even if it's a wrong word. Being able to see the letters laid linearly is useful to solving. Automated clearing of wrong words is unhelpful.
murphyslab··on I don't understand graphical abstracts. So I both hate and admire this one (2025)
> I have never, ever – not even once – seen a graphical abstract that usefully “summarized the contents of an article”.

The author has never worked in chemistry. They are absolutely ubiquitous in scholarly journals for chemistry and I'd say that most people trained in chemistry often only read the graphical abstract when initially deciding whether the paper is worth a deeper read. Perhaps chemistry is a naturally visual field, given that we rely on visualizations of reactions and mechanisms from the very start of our university education.

The table of contents (TOC) graphic usually shows a key chemical structure (thus bonding connectivity, angles, elements, and electronic configurations), reaction mechanisms or conditions, models, or even core results as graphs. Now I do not claim to understand what is implied in every TOC graphic, however I can immediately see which branches of chemistry the article relates to faster than I can process the title, especially in a multidisciplinary chemistry journal.

That ability to categorize to identify relevance is a bigger issue in reading a multidisciplinary chemistry journal like the Journal of the American Chemical Society:

https://pubs.acs.org/toc/jacsat/current

But graphical abstracts are still immensely useful within a subdiscipline such as organic chemistry, which I suspect were the early adopters of TOC graphics:

https://pubs.acs.org/toc/joceah/current

The better graphical abstracts tend towards simplicity, but it's a challenging task to distill a year or more of research into a single picture. And, unfortunately, graphic design is not a subject for which scientists generally receive additional training, despite it being a core element of digital communication.

murphyslab··on New accounts on HN more likely to use em-dashes
A Bonferroni correction would be suitable. I usually see it used in genome-wide association studies (GWAS) that check to see if a trait or phenotype is influenced by any single nucleotide polymorphisms (SNPs) in a genome. So it's doing multiple testing on a scale of ~1 million.

> One of the simplest approaches to correct for multiple testing is the Bonferroni correction. The Bonferroni correction adjusts the alpha value from α = 0.05 to α = (0.05/k) where k is the number of statistical tests conducted. For a typical GWAS using 500,000 SNPs, statistical significance of a SNP association would be set at 1e-7. This correction is the most conservative, as it assumes that each association test of the 500,000 is independent of all other tests – an assumption that is generally untrue due to linkage disequilibrium among GWAS markers.

https://journals.plos.org/ploscompbiol/article?id=10.1371/jo...

cf: https://en.wikipedia.org/wiki/Bonferroni_correction

murphyslab··on Canada's Carney called out for 'utilizing' British spelling
One persistent problem is that there isn't a Canadian English spelling option in most software with spellchecking functionality. Often we are forced to choose between US English and British English spelling defaults, when neither is quite right. I suspect that this was a stylistic choice not of Carney himself, but whoever proofread the document. There has been considerable erosion in Canadian orthography in of late, which has only been made worse with the widespread adoption of UFLI English language learning materials in our schools' elementary curricula, which emphasizes American spelling and pronunciation.
murphyslab··on All life copies DNA unambiguously into proteins. Archaea may be the exception
Paper: https://doi.org/10.1073/pnas.2517473122 (Open Access)
murphyslab··on Show HN: An easy-to-use online curve fitting tool
Not to cast shade, but it looks like you've essentially built a front-end for Desmos. It definitely makes things faster than trying to do it directly in Desmos.

Suggestion: Most of the fits that you've done assume that the errors are normally distributed. It would be worthwhile adding some graphical or numerical checks on that, rather than having goodness of fit or visual inspection be the only indication if this is a faulty assumption.

It gave made for a good quick check testing some data I had.

murphyslab··on Show HN: An easy-to-use online curve fitting tool
Copy-paste worked perfectly for me. I just copied 16 data points I had in an open G Sheets tab and used the "Batch Add" button.
murphyslab··on Show HN: I've build a platform for writing technical/scientific documents
LaTeX was much easier with Overleaf for my PhD thesis. I still recommend that for friends starting a thesis or a book project. I even used it for recent book project with a friend.

As you noted, one needs a lot of fine tuning to meet publication rules & guidelines. Compared to a local LaTeX editor or Overleaf, this looks too generic to meet the needs I've had in the past. Sure, LaTeX can require a lot of tinkering, but PhD students ought be able to figure it out for themselves, whether through documentation, forums, or asking labmates.

murphyslab··on YouTube says it'll bring back creators banned for Covid and election content
Two articles that I found offered a well-rounded analysis:

- https://www.engadget.com/big-tech/youtube-may-reinstate-chan...

- https://arstechnica.com/gadgets/2025/09/youtube-will-restore...

murphyslab··on Tech companies are telling immigrant employees on visas not to leave the U.S.
It's what their lawyers are advising them.

The Globe and Mail had a piece on March 25th on the advice that lawyers were giving to their clients, often Canadians working on TN visas down south:

> York-based immigration law firm Dyer Harris LLP, which helps foreigners secure work visas in the U.S., sent an e-mail to their clients residing and working in the country to hold off on international travel altogether, unless in an emergency.

Lawyers advise Canadians working in U.S. to avoid travel amid border crackdown, The Globe and Mail, 2025-03-25. https://web.archive.org/web/20250325223021/https://www.thegl...

murphyslab··on Common food dye found to make skin and muscle temporarily transparent
UV damage to internal tissues seems unlikely given that the tartrazine dye they used absorbs strongly in the UV region of the spectrum. You can see this in Figure S1 A & B:

https://www.science.org/doi/suppl/10.1126/science.adm6869/su...

Also the abstract of the article notes that strong UV absorption is likely a prerequisite for this effect:

> We hypothesized that strongly absorbing molecules can achieve optical transparency in live biological tissues. By applying the Lorentz oscillator model for the dielectric properties of tissue components and absorbing molecules, we predicted that dye molecules with sharp absorption resonances in the near-ultraviolet spectrum (300 to 400 nm) and blue region of the visible spectrum (400 to 500 nm) are effective in raising the real part of the refractive index of the aqueous medium at longer wavelengths when dissolved in water, which is in agreement with the Kramers-Kronig relations. As a result, water-soluble dyes can effectively reduce the RI contrast between water and lipids, leading to optical transparency of live biological tissues.

https://www.science.org/doi/10.1126/science.adm6869

However this kind of research into the effects of absorption bands on the transmission properties at interfaces might ultimately bring about more effective sunscreen formulations.

murphyslab··on Big Pharma claims lower prices means giving up miracle medications. Ignore them
You cannot always obtain a generic version; sometimes not even the original version.

Drug manufacturers regularly take approved medicines, which are off-patent and non-exclusive, due to safety reasons (side-effects, risks to patients) or due to commercial reasons: high cost of production, low demand, or possibly to increase demand for an exclusive alternative.

The FDA maintains a list of "List of Off-Patent, Off-Exclusivity Drugs without an Approved Generic": https://www.fda.gov/drugs/abbreviated-new-drug-application-a...

See also: https://en.wikipedia.org/wiki/List_of_withdrawn_drugs

There are also perverse incentives at play and it often isn't easy to get a generic approved, especially if the original drug was already removed from market, under biosimilar regulations:

https://prospect.org/health/2024-03-14-novo-nordisk-disconti...

murphyslab··on Moments in Chromecast's history
> With this, there are no changes to our support policy for existing Chromecast devices, with continued software and security updates to the latest devices.

"no changes to our support policy" links to https://safety.google/nest/

It bothers me when these company blogs link to the wrong page for finding the aforementioned policy. It feels so deceptive. I've seen it happen multiple times. Is it intentional?

murphyslab··on Japanese chemistry institute sues CLOCKSS for hosting discontinued journal
Japan Institute of Heterocyclic Chemistry, the publisher of the journal Heterocycles (1973-2023) [0] is suing CLOCKSS, after its content was released on June 25, 2024 [1]. All of the content from Heterocycles had ceased being available online, and per their agreement with CLOCKSS Archive in 2011,[2] all of the journal's 106 volumes have been made available under the CC BY-NC-ND 4.0 license.[3]

For how this works, see "How CLOCKSS Works" [4] & "How LOCKSS Works" [5].

Chemistry World also had an earlier article ("A key chemistry journal disappeared from the web. Others are at risk", 2024-04-09 [6]) discussing the journal's sudden disappearance [7] and the loss of access when it went offline, an increasingly common problem with scholarly research.

[0]: https://en.wikipedia.org/wiki/Heterocycles_(journal)

[1]: https://clockss.org/clockss-triggers-heterocycles/

[2]: https://clockss.org/the-japan-institute-of-heterocyclic-chem...

[3]: https://clockss.org/triggered-content/heterocycles/

[4]: https://clockss.org/about/how-clockss-works/

[5]: https://www.lockss.org/use-lockss/how-lockss-works

[6]: https://www.chemistryworld.com/news/a-key-chemistry-journal-...

[7]: https://web.archive.org/web/20240217181955/https:/www.hetero...

murphyslab··on That Editor
You claim, as a "fact", that someone who wrote this [0], identifies as Jewish?

[0]: https://bisqwit.iki.fi/jesus/

murphyslab··on A new world of DIY medical testing
> in a malpractice situation, a physician could be liable if they made diagnosis or treatment decisions based on unverifiable LDTs.

That seems to be a senseless concern, since offered the evidence of a lab test, a physician should be prompted to investigate further. No physician (nor individual) should ever be making a diagnosis or treatment decision based on a single line of evidence.

More importantly, such results can help offer hard evidence to pressure one's physician to investigate a particular complaint, which can be difficult to convey or to convince the physician it's real. Physicians are often dismissive of things that they do not understand, or of certain classes of patients. Consequently many patients are forced to figure out the source of the problem for themselves.

With a lab based test result, you can go to a physician and say, "Hey, this isn't just my imagination nor some kind of over-reaction. It's tangible and externally verifiable."

And for those without a GP, waitlisted like myself (5+ years waiting here in Canada!), such tests can help one navigate our piecemeal medical system more effectively.

murphyslab··on Why are debut novels failing to launch?
The Dungeon Crawler Carl series' first 4 or 5 books (it's been a little while) were excellent. Carl's tone reminds me of a detective novel, while the setting is more reminiscent of Ready Player One and The Matrix. The genre is a LitRPG novel (admittedly a genre I'd never known existed until reading DCC), heavily doused with comedic elements. Lots of mature themes and references to sex, drugs, politics, and violence, but with some of the allegorical or illustrative critique (to the point of absurdity) you'd find with Douglas Adams or Terry Pratchett when discussing serious topics with parallels to real life, in an imagined scifi/fantasy setting. I'd recommend the series if for those who haven't picked up a book in a while and who would appreciate those elements.
murphyslab··on Show HN: Huewords, a Word and Logic Puzzle
Fun game, although it would be helpful to have the "How to Play" instructions ( https://huewords.snellman.net/help.html ) explicitly state that shorter letter sequences (2,3,4 letters) do not need to form words. That's an expectation built up from many other crossword games, so it would be good to nullify it through a clear statement that the usual crossword rules do not apply here.
murphyslab··on Gone 10 years, World’s Biggest Bookstore still grips readers
I remembering visiting WBB at 20 Edward St when I lived in the GTA during a co-op term. But the real treasures I found were usually in BMV Books next door at 10 Edward St. BMV offered incredible collection of vintage books and magazines. I recall the owner guaranteeing to me that he could find any book sold at WBB and get it to me cheaper. Glad to see that it's still standing.
murphyslab··on Reddit's long, rocky road to an IPO
> a non trivial expense that's hard to entice enough users to cough up money for to make viable

Yet the site's operators got rid of one of the most popular mechs for monetization: Awards.

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