gilleain

6 ms·

61.
by gilleain 4mo ago
Yes, I was watching a video about that the other day - the 'dark proteome' or the 'ghost proteome' or similar.
62.
by gilleain 4mo ago
A random sequence may not fold at all! I seem to remember a paper that tried this, creating a bunch of random proteins, and checking how much structure they had - I think they were helical bundles, but don't quote me. The nice thing a
63.
by gilleain 4mo ago
I see. I meant 'energetically accessible', but you mean more like 'affordably accessible' (in the sense that the molecular toolkit of a cell is what can 'afford' certain structures, due to chaperones available
64.
by gilleain 4mo ago
This is about folds, not amino acids - even if you used a larger alphabet of residues, I somehow doubt that you would get many more folds. Thinking more about the question of protein _length_ - I'm also not convinced that longer protei
65.
by gilleain 4mo ago
I understood it as metaphor - just that evolutionarily distant sequences can adopt the same (or very similar) folds because there are only a limited number of stable, accessible folds that are possible.
66.
by gilleain 4mo ago
They found "several thousand" novel folds? I had remembered that there were around 1000: https://pmc.ncbi.nlm.nih.gov/articles/PMC7072414/ Oh ok, I misremembered: "This review has focused only on sm
67.
by gilleain 4mo ago
Ah FeMo-co! One of the cooler cofactors - iron-sulfur cluster, plus a molybdenum, and finally a bridging carbon ( https://en.wikipedia.org/wiki/FeMoco ) So yes, I can understand why it took so long to calculate the energ
68.
by gilleain 5mo ago
Hate to agree, but it is true. For a while, I think, the main sequencing framework was in perl (Bioperl). Not sure what was best for structures - possibly Biojava? It is very tempting, though - 'just' make a nice, clean API in you
69.
by gilleain 5mo ago
DNA is one-dimensional aperiodicity, which is ... fairly common. This sentence is one-dimensionally aperiodic! Most biological structures are amorphous in some way, rather than strictly aperiodic. There are structures (honeycombs, for examp
70.
by gilleain 5mo ago
More than that - I think that people who are grieving may not know how they "should" be grieving. Consider that some cultures (literally) perform grief by - for example - wailing at the grave. Others may wear a particular colour o
71.
by gilleain 6mo ago
'The presenter' here being Eddie Izzard :)
72.
by gilleain 6mo ago
Yes I thought at the start it was about how our expectations of how the law works are at odds with the reality So the gatekeeper is the system keeping us from Justice - mostly money, but also other less tangible barriers. In theory, everyon
73.
by gilleain 6mo ago
Well, the image titled 'The Shapes of Water' has 4 examples - 'Ice Ih', 'Ice VIII', 'Ice XV', and ... 'Ice IX' :) https://en.wikipedia.org/wiki/Phases_of_ice#Known_phase
74.
by gilleain 6mo ago
That's fair (and of course, as a personal project, set any goal you like! :) ) - but I wonder if that risks setting the bar too low, so that everything is 'completed'. I think, we're in agreement : it's your project
75.
by gilleain 6mo ago
Also it can give a feeling that it was not a waste of time - lessons learned, what you would do next time on other projects, other avenues to look into. For years I wrote a technical blog intended just for my own reference, as the small eff
76.
by gilleain 6mo ago
I accept the ordering of dates is important, yes. History can be in the details, but as you say you need to comb the beach for the right stones. I guess an interesting counterpoint to what I said is something like https://en.wiki
77.
by gilleain 6mo ago
Yes I was not clear, it seems. Facts are necessary but not sufficient. There is limited time, of course - no one can learn everything, but you can pay attention to the important facts, and the connections between them. In some ideal world y
78.
by gilleain 6mo ago
Agreed, it interests me how much some people emphasise knowing facts - like dates in history or dictionary definitions of words. Facts alone are like pebbles on a beach, far better (IMO) to have a few stones mortared with understanding to m
79.
by gilleain 6mo ago
I've revived a project I started around 20 years ago. It is a kind of graph query description/measurement tool for protein 3D data. The query engine itself is like a DAG of 'operators', similar to a relational DB (or mor
80.
by gilleain 7mo ago
... but have you considered the new ballroom?
81.
by gilleain 7mo ago
Not precisely the same: https://en.wikipedia.org/wiki/Hydrogen_cyanide - 107 ppm (human, 10 min) https://en.wikipedia.org/wiki/Hydrogen_sulfide - 600 ppm (human, 30 min) https://en.wiki
82.
by gilleain 7mo ago
Not an answer, but related, I was looking at Memgraph (graph db) query planning for Cypher, which is similar (ish) to what you are asking about: https://memgraph.com/docs/querying/query-plan The reason why I was l
83.
by gilleain 7mo ago
Someone's artwork _should_ be possible to (negatively) criticise. Of course, just saying "it sucks" is not constructive or helpful. You can definitely hurt someone's feeling with unconstructive criticism of thier art. Ho
84.
by gilleain 8mo ago
Cyclopentadiene is a great molecule - it can form 'metallocene' compounds where two cyclopentadiene (Cp) rings 'sandwich' a metal ion between them: https://en.wikipedia.org/wiki/Metallocene Like Cp-
85.
by gilleain 8mo ago
Bring on the Electric Monks ...
86.
by gilleain 8mo ago
Or by the 'Chaos Star' :) https://en.wikipedia.org/wiki/Symbol_of_Chaos
87.
by gilleain 8mo ago
Oh that reminds me. Could someone make an AI interface where each agent uses a different Culture ship name, and looks like the dialog from Excession? If we are going to have a dystopia, lets make it fun, at least...
88.
by gilleain 8mo ago
I've had reasonable results from using AI to analyse code ("convert this code into a method call graph in graphml format" or similar). Apart from hallucinating one of the edges, this worked reasonably well to throw this into
89.
by gilleain 8mo ago
> The same people who brought back witching burning Seems like it was more complex than that : > Authors have debated whether witch trials were more intense in Catholic or Protestant regions; however, the intensity had not so much to
90.
by gilleain 8mo ago
> BTW, the mentioning of HF will likely horrify chem-phobic readers I would not say I am chem-phobic, but yes indeed that stood out. HF is nasty stuff, and yes requires some care I suspect. The other details are fascinating, though - the

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