theophrastus

After spending an entire career doing 'by hand' (and a helluva lot of molecular orbital calculations) on the problem this post is about, i've got to tersely weigh in with: there's (still) not enough available data given the size of protein 'phase space' to hope for a proper covering with one's trained up linear algebra model. Or typed another way: you've got to include at some stage some physical modeling parameters, like molecular orbitals [1], otherwise the 'response curve' will only optimize if one gets quite lucky, (which is actually unlucky as then you'll delude yourself into thinking it's a generally applicable, which it isn't). For instance, swap in a carboxylic acid moiety where there was previously an aldehyde, a protein side-chain flips over, and you're in a completely different corner of the energetic 'galaxy'.

[1] e.g. https://proteindf.github.io/

Jameco sells one [1]

[1] https://www.jameco.com/z/KIT-EFK-BUNDLE-Jameco-Kitpro-Compon...

Had a QuantSci Prof who was fond of asking "Who can name a data collection scenario where the x data has no error?" and then taught Deming regression as a generally preferred analysis [1]

[1] https://en.wikipedia.org/wiki/Deming_regression

Merry Christmas!! you gentle nerds you! Peace to us all.

What was the source of the oxygen to maintain ethyl alcohol combustion in a sealed WWII torpedo?

Curiously the default has audio output off. That is, was the little speaker icon unmuted?

Here's from 2014 with some capacity calculations [0]. "ssh private key (900 bytes): 15 feet of tape."

[0] https://heepy.net/index.php/Data_storage_capacity_of_teletyp...

Circa 1980, as a hobbyist beekeeper with six hives nearby Seattle, they came down with foul-brood. (It never was certain if it was American Foul-brood or European) Duly reported and the county agent came in, sealed them, and carted them away. For an additional fee (which I paid) they would fumigate them and return just the hive bodies, but none of the frames, (some of which would contain the infected brood). Those were burned. I believe the fumigant at the time was phosphine[1]

[1] https://en.wikipedia.org/wiki/Phosphine

Shouldn't this make some initial direct reference to the author: Silvanus P. Thompson[1]?

[1] https://en.wikipedia.org/wiki/Calculus_Made_Easy

Additional small molecule pharmaceutical candidates via molecular descriptors

Well done: 3d is an option! Always wondered what emergent properties result from simple rules worlds when the dimensionality goes from 2d to 3d.

Lately in advertisements there have been a lot of circular QR codes[1]. Which often apparently present data outside of the alignment patterns. Is that merely an artistic device, or is there some standard permitting information extending beyond the square region?

[1] https://www.google.com/search?tbm=isch&q=circular%20qr%20cod...

..and curiously, with the little speaker icon 'on', it produces no audio alarm for me, (firefox 103.0.2). Whereas this[1] one produces a quite notable sound.

[1] https://www.online-stopwatch.com/countdown-timer/

As more of a story of external impressions, i'm from Seattle and I postdoc'ed in Germany and I got more than my share of the opinion on English from those who could speak English there (damn near 100% at a University). The first problem they had was placing my accent; they couldn't. Finally they concluded that i was some-sort of Canadian (which is pretty accurate). Then they did their own versions of U.S. accents. Almost universally these divided into New York and Texan. Their impression of the states, based on either vacationers or hollywood, confirmed their view that people from the U.S. were either loud with a Texas accent or loud with a New York accent. We decided that it was a natural sampling bias based on the overhearing of the loudness.

After gmail recently greeted my mutt/IMAP request (which had worked perfectly for over a decade!) with "login failed", i've embarked upon the slow winding road to getting mutt to use OAuth2, or is it OAUTHBEARER?, for gmail. Out of a dozen or so hints spanning the last couple of years (many which depend on having python2 still around), i'd humbly promote these links to best hints:

[1] http://www.dcs.gla.ac.uk/~jacobd/posts/2022/03/configure-mut...

[2] https://www.reddit.com/r/backtickbot/comments/kyuq11/httpsnp...

Please post any better sites you discover. It really is an overly server specific mess.

from the web-page:

    It does not require training data - instead it uses statistical information about the frequencies of the letters and n-grams in the English language.

and from this it should also be noted that it won't apparently be able to extract passwords, as least those which aren't "n-grams in the English language".

Well it goes the other way too. English to arcane C declaration. And that's what many of us have used it for decades (and decades...). Try:

    declare xyzzyx as pointer to pointer to array 153 of const double

So this results in a single wavefunction constrained to a particular space group[1]?

[1] https://en.wikipedia.org/wiki/Space_group

At some point in every bioinformatics lecture i always manage something akin to: "Learn awk! (or perl) You'll need it. Your data will come from various disparate sources, and you need to get them into some well-defined useful format from the get go."

A layman's speculation followed by a layman's (at least in terms of immunology) question: introduce a novel mRNA, cells produce novel protein, it is presented to the immune system as something to foment a defense again: vaccine. But the article talks about using this mechanism to replace a functional copy of a genetically missing enzyme. How is it assured that this will assume the opposite goal and not become another target for the immune system to guard against?

My 89 year old mother loves to tell the story of her brother and friends spending several hours getting whatever body part they could push through the shoe slot below to be reported on how it looks by another child looking through the scope at the top. They were very disappointed that my uncle's head couldn't fit so they could examine his brain, (which they always figured had some bats in it)

"LWN recently covered the effort within the LibreOffice project to find ways to support the companies doing the bulk of the development work. The project has now posted a revised marketing plan [PDF][2] with a number of changes, including the removal of the "personal edition" name. Regarding LibreOffice Online: "Following our normal development process, the Ecosystem will release their own versions in their own timing, allowing some features to reach their Enterprise versions before they are subsequently shipped in TDF builds (this allows the Ecosystem to positively differentiate by contributing new features & functionality)".

[1] https://lwn.net/Articles/826217/

[2] https://nextcloud.documentfoundation.org/s/4pLtn9xn76BkxFK#p...

This couldn't be the leakage from that nuclear powered cruise missile 'test' lost by the Russians 2017-2018[1]? That is, is Barents sea too far from the Baltic for a couple of years of tides?

[1] https://www.theverge.com/2018/8/21/17766426/russia-nuclear-p...

A chemical catalyst is an agent which lowers the activation energy for a reaction to proceed. A biochemistry professor of mine was fond of declaring life to be an entropic catalyst.

My point of view on this is from a career as a protein x-ray crystallographer, not a mathematician nor computer scientist. I've watched countless tiny crystal dishes, the vast majority of which produce no useful crystals. And while it seems frustratingly random, (especially when faced with months and years of failure), in retrospect from a successful series there are always conditions which likely make causative sense: changes in temperature, stocks of substituent additives, shifts of pH due to carbon dioxide in the air, vibration (or lack thereof) from nearby construction or robotic systems, amount of pollen or air pollution to add nucleation sites. Some crystals will only form along the edges of the crystal dishes; perhaps because there's some complementary dimensions of the molecular surface there. It's a rich list of possibilities, but all would speak against this being as 'random' as say, the exact time of the emergence of an x-ray photon from our source. Nonetheless it's a very creative use of a lot of otherwise non-useful data from vast arrays of robot observed crystallization dishes.

This is a worthy posting, particularly as so much becomes iterative statistics in "A.I." clothing. The two old (slightly hackneyed) counter-examples which are popular in lectures about measures of the central tendency are:

- One is trying to get a sense of the common sort of income in a room and then Bill Gates wanders in. Suddenly the average income becomes an amount which no one experiences.

- What is the average number of testicles in the human population? That computed central tendency is quite rare.

Old radios too [1]. A few years back there was an intense discussion on some antiquarian site about what the function was for a central hole in an otherwise beautiful antique wooden philco radio cabinet. Finally some bright old duffer shows up and allows: "Oh, that's where the 'magic eye' went". Of course, the rest thought he was just pulling their legs about there being a "magic eye" on these things.

[1] https://mikesradiosandstuff.weebly.com/uploads/1/0/8/7/10875...

This is a very impressive site for teaching molecular file formats indeed! If there is one caveat that an old crystallographer might add...

  press ENTER, the 2D and 3D structures will update. 

When going from the 2d connectivity graph to 3d there arise essential emergent properties, some of which can be specified, like stereochemistry (left or right chirality), and some which can be estimated with a lot of theory and additional calculation like multiple conformers (e.g. trans and cis), and thermal preferences (staggered vs eclipsed along rotable bonds), and onwards to intensive quantum chemistry for electron distribution which is so critical for design for enzyme binding. That is, "3d" at this level is very much an approximate single still image of a very dynamic system.

That's impressive; and for me a bit reminiscent. I got my doctorate staring at macromolecular structures through various attempts at presenting them in 3d. One of the earliest I encountered was called a "Richard's Box"[0]. That setup was a set of clear plastic sheets on which were plotted 'slices' of electron density which were subsequently stacked-up with suitable sized spacers and you looked down through the stack with an lamp beneath. This approach sounds very similar, but with an active display in place of each sheet of plotter output.

[0] https://www.umass.edu/microbio/rasmol/history.htm

"Researchers in Japan and at the University of Michigan said Monday that they had found a way to take over Google Home, Amazon’s Alexa or Apple’s Siri devices from hundreds of feet away by shining laser pointers, and even flashlights, at the devices’ microphones."