gilleain

38 ms·

511.
by gilleain 4y ago
Oh ok, looks like this is called the https://en.wikipedia.org/wiki/Bucherer%E2%80%93Bergs_reactio... - mentioned in the abstract.
512.
by gilleain 4y ago
What looks like the main (?) reaction (from the graphic on https://www.nature.com/articles/s41557-022-00999-w ) : R-C(=O)COO -- (CO2, "NH3", CN-, H2O) --> R-Hydantoin (?) --> aminated amino acid --> a
513.
by gilleain 4y ago
You're right in focusing on the diversity of the parts. After all, a large pile of sand has a lot of parts, but they are all (to a decent approximation) the same. Therefore (?) they have the same small set of interactions, and the whol
514.
by gilleain 4y ago
Heh, I'm somewhat the opposite, as I went from a degree in biochemistry into bioinformatics (protein folds and structure) and have an amateur interest in maths. I often recommend the book 'Cats' Paws and Catapults' by St
515.
by gilleain 4y ago
Yes, very much so. Even for proteins that seems like they are just scaffolding for a catalytic centre can have important dynamics. A classic example is haemoglobin, that 'just' binds to oxygen at the iron in the middle of the haem
516.
by gilleain 4y ago
Fair point. I guess if their training data is biased towards existing known structures (via xray or nmr or whatever) then there is the risk of incorrect predictions. At a guess, the core packing in non-globular proteins might be different?
517.
by gilleain 4y ago
edit: I should have read the post first! What do you mean 'only globular proteins'? They say they have predictions for all of UniProt... --------------- Yes, the idea of a 'protein universe' seems like it should at least
518.
by gilleain 4y ago
As a simple example, one measure used to compare a predicted structure against a reference is the RMSD (root mean square deviation). https://en.m.wikipedia.org/wiki/Root-mean-square_deviation_o... The lower the RMSD be
519.
by gilleain 4y ago
The other great feature were 'nodeshells' (that is, links to pages that did not yet exist). These could act as writing prompts, or just as a way to 'comment' on other nodes (pages). Weirdly, one of the ones I liked (by a
520.
by gilleain 4y ago
From an interview I read a couple of years ago, this part stuck out (paraphrased, from memory). The interviewer asked something like "Are you optimistic about human survival?" and Lovelock's reply was, roughly - "Oh yes,
521.
by gilleain 4y ago
Thus my friend's idea to CRISPR plants so that they deposit their carbon in some indigestible polymer that will not rot for the foreseeable future. I'm sure there are no possible repercussions to doing this.
522.
by gilleain 4y ago
The simple answer is that I don't know! I never looked at 'normalization' in graphs. From a quick google, seems like it has been used in a couple of contexts. Firstly in GNNs which I definitely know nothing about. However I s
523.
by gilleain 4y ago
I guess it might be 'graph hashing', also known as canonicalization. So this is related to some other things, like the Weisfeiler-Leman Algorithm, and Morgan numbers, and partition refinement. The idea is that to compare two graph
524.
by gilleain 4y ago
I must be running on slower code, as I can't quite unpack that. So the code in life is the DNA which is also the 'runtime'?
525.
by gilleain 4y ago
Er, hate to nitpick but photosynthesis uses magnesium, no? In the chlorophyll, at least, although other parts have haems with iron in :) (Also as with anything in biology, there is no doubt some weird organism that has like a cadmium or sim
526.
by gilleain 4y ago
I worked for a professor (James Milner-White) who was interested in early protein evolution and I remember a conversation we had about the possibility that proteins could have evolved from large to small. Not sure if it was from a published
527.
by gilleain 4y ago
Great description. I would go further to describe living systems as not just distributed and so on. Also they are self-assembling and self-repairing. They are redundant - which makes them more damage resistant and 'evolvable'. Als
528.
by gilleain 4y ago
How were they lost or rediscovered? "Muhammad ibn Zakariya al-Razi (Latinized: Rhazes) (born 865) was one of the most versatile scientists of the Islamic Golden Age ... Many of his books were translated into Latin, and he remained one
529.
by gilleain 4y ago
> The wiki seems to indicate not except the book of optics? Not sure how you reached that conclusion. Perhaps it would be helpful to search for 'Latin' in that wiki page. There's a reason why so many of these Islamic figur
530.
by gilleain 4y ago
Yes, indeed. I understand that some editions of D&D are considered class-unbalanced because high level mages are so powerful. When one member of the party can stop time, call down meteors or kill with a word then just being able to swin
531.
by gilleain 4y ago
Yes, that would be obnoxious ... if that's what they said :) To be clear, I don't like it either if others consider their taste to be 'superior', but simply stating what you prefer is not - I think - implying anything. I
532.
by gilleain 4y ago
Most hilariously (to me) is the vast difference in 'powers' between superheroes. There are the 'Gods' - some literal, like Thor, or godlike otherwise - and the 'normals'. Gods can fly, shoot lasers from their e
533.
by gilleain 4y ago
But they are not? They are expressing their opinion on a type of movie. Why is that 'denigration'?
534.
by gilleain 4y ago
Yes, I looked into this a few months ago. The cheapest I could find were 'robot' plotters that actually move across the paper. Not as accurate as I would like. The alternatives seemed in the £100-500 ($120-620) range.
535.
by gilleain 4y ago
I use flat magnets in pairs - like neodymium ones, but disc shaped. Like these (although I don't know the exact brand of mine): https://www.eclipsemagnetics.com/products/magnetic-tools-and...
536.
by gilleain 4y ago
Thanks, that looks very helpful. I have a 'Pocket color wheel' that works ok, but I see that link has a more sophisticated division of color space. Nice!
537.
by gilleain 4y ago
what does fluoride do to watercolors?
538.
by gilleain 4y ago
It's good to read books on how to do it, of course. However, I started out a couple of years ago just making small pictures as quickly as possible over lunch. If you don't set too high expectations, it's great to just experim
539.
by gilleain 4y ago
This all seems like sound(er) advice. On color : I recently realised (or read somewhere) about the simplest color wheel- if you divide a circle into 6 segments and paint the primaries : {R, Y, B} in non-neighbouring segments, then the ones
540.
by gilleain 4y ago
There is also selenocysteine, which is cys with the sulfur replaced by selenium. https://en.wikipedia.org/wiki/Selenocysteine It's not present in all organisms, but where it is, it is incorporated in proteins duri

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