Computer simulations suggest human proteome is close to optimal

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funkervogt
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Computer simulations suggest human proteome is close to optimal

Post by funkervogt »

Perhaps you can get similar overall structures from very different sequences - and that turned out to be the case here. Using AlphaFold to predict the structure of the new artificial sequences showed that they roughly matched known lyzozymes in three dimensions, and that was the case for the low-sequence-identity ones as well. In this case, then, we see that there are far more ways than are known in nature to arrive at more or less the same place, structurally (and functionally).

You’re very likely not going to be able to use these techniques, then, to arrive at totally new protein folds doing totally new things. But you can expand what’s known about the pathways that evolution didn’t take. It’ll be interesting to see if some protein classes are more constrained than the lysozymes, for example, and some of them surely are. As an extreme example, consider the photosynthesis protein RuBisCO, which by enzymatic standards just barely seems to work at all and has proven spectacularly difficult to improve by mutation or computational design (but is nonetheless the keystone for most of the life on the surface of the earth). I would not expect to generate a big ol’ list of alternate RuBisCOs, because it seems to be wedged into a pretty tight slot already.
https://www.science.org/content/blog-po ... g-proteins

This has implications for the future of human genetic engineering. Simply put, we might not be able to improve our proteins much. Separately, I've read that the human genome is, in spite of what is said about a huge portion of it being "junk DNA," pretty efficient. Even the structures of our nucleic acids are maximally efficient.
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Yuli Ban
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Re: Computer simulations suggest human proteome is close to optimal

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I've thought about this too, hypothesizing that there might be a biological asymptote that we are already near.

In fact, somewhat related, I've wondered if there might be a "great asymptote" of science and engineering where even ASI cannot meaningfully improve beyond it, and that a Singularity-like point will occur before very rapidly plateauing once ASI figures everything out.

Needless to say, "asymptote" is a word that's been nagging me a lot lately and which I fear will greatly upset a lot more people in the coming years.
And remember my friend, future events such as these will affect you in the future
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ººº
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Re: Computer simulations suggest human proteome is close to optimal

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^ More reasons to take care of this planet as we will be stuck here for the next 1000-2000 years until terraformation is completed.
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funkervogt
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Re: Computer simulations suggest human proteome is close to optimal

Post by funkervogt »

Yuli Ban wrote: Tue Feb 07, 2023 4:38 pm In fact, somewhat related, I've wondered if there might be a "great asymptote" of science and engineering where even ASI cannot meaningfully improve beyond it, and that a Singularity-like point will occur before very rapidly plateauing once ASI figures everything out.
Impossible to know. If there is, then at least we'd be assured there wouldn't be much of a power difference between us an aliens that discovered space flight 100 million years ago.
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