#alphafold

the goal of this blog is to use the strings of letters from text posts matching proteinogenic amino acids into 3D structures using AlphaFold. i am not affiliated with AlphaFold in any way, just using it to create and share some neat images. the idea for this was heavily inspired by @hellsitegenetics .

to make these, i will be removing any letters not matching proteinogenic amino acids, as well as any other characters, and plugging the resulting sequence into AlphaFold3. while i tried in some early posts, unusual amino acids unfortunately do not work in my structures. therefore, B, J, O, U, X and Z will all be omitted. in the final image i will usually only be showing the cartoon and hide the surface and side chains, for the sake of making a somewhat more pleasant image. i now use ChimeraX to open and show structures. they may not always be accurate depending on the string of letters, so unless i say anything else, assume that none of it is reliable!

also disclaimer: i am not a structural biologist (i have a bachelor’s degree in biochemistry and am currently studying lipids). i will do my best to answer questions but i will surely make mistakes. please correct me when this happens!

please send me any posts you want to see made into structures :) i can't promise i'll answer fast but i will do my best

some of the more popular protein memes:

never gonna give you up, leitner rant, bee movie intro, spiders georg, ihnmaims hate, man door hand hook car door

and of course: the full bee movie script

here are some tags i tend to use to categorize things:

#protein asks for inbox submissions

#protein memes and #protein songs for memes and songs

#protein info if i'm answering science questions or explaining things

also, here is the colour scale for pLDDT scores. most of the structures on here are solidly in the orange and red areas, so i don't usually post these

AI could short circuit the process of building human understanding, which is essential to scientific progress ————

AI might prolong the reliance on flawed theories.

How was the geocentric model of the Universe overturned in favor of the heliocentric model — the model with the planets revolving around the Sun? It couldn't be resolved by comparing the [mathematical] accuracy of the two models, since the accuracy of the models was similar. Rather, it was because the heliocentric model offered a far simpler explanation for the motion of planets. In other words, advancing from geocentrism to heliocentrism required a theoretical advance, rather than simply relying on the more accurate model.

This example shows that scientific progress depends on advances in theory. No amount of improvements in predictive accuracy could get us to the heliocentric model of the world without updating the theory of how planets move. (...)

If AI allows us to make better predictions from incorrect theories, it might slow down scientific progress if this results in researchers using flawed theories for longer. In the extreme case, fields would be stuck in an intellectual rut even as they excel at improving predictive accuracy within existing paradigms.

Aging is a disease, the most lethal of them all. People are realizing this and working to find solutions fast. We will look back in utter disbelief, shock, that we allowed this to go on for as long as we did. Realizing that the pain, suffering of losing a loved one to age, and that it was preventable, will be a permanent stamp of failure on the human race. It is haunting to even think about now. Even with population increases (we’re going the opposite way right now) the dead::alive will remain increasingly negatively correlated until we solve this.

If you think we’re in the red zone re: growth in longevity biotech above, which could be valid, & you think you’ll miss it all by about the length of time of an average lifespan of today, the answer is simple: cryonic storage when you’re at your final points of life. I don’t think we’ve made enough progress to ensure continuity of life on the other side yet, so it’s not realistic today, but by 20-80 years, easily possible.

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We’re in an exponential growth phase, but we’re nowhere close to the top. It’s accelerating hard now.

CEO @ OpenAI, Sam Altman reinforces my thinking here.

“On a zoomed-out time scale, technological progress follows an exponential curve. Compare how the world looked 15 years ago (no smartphones, really), 150 years ago (no combustion engine, no home electricity), 1,500 years ago (no industrial machines), and 15,000 years ago (no agriculture).”

Take 10 minutes to think about what your life would be like if death wasn’t guaranteed. After the first 10 minutes are spent in shock/denial/absurdity of it all, take another 10 to really think about the possibilities.

“The greatest shortcoming of the human race is our inability to understand the exponential function.”