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One sort of “rule” I’m working with in my world is that among carbon-based, protein-having species, even those from different planets with no shared evolutionary ancestry, proteins that may be composed of different analogous sets of amino acids still fold into the same overall shapes, paralleling each other in structure when they have the same function (especially since shape often decides function for a protein) regardless of their specific biochemical makeup. In short, protein shapes that perform the same function are highly conserved across species, even those not related. What sort of explanation might suffice to cover why this degree of conservation would occur for reasons other than a shared evolutionary history? Is it enough to say that “same function = same shape” even across different planets like that?

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  • $\begingroup$ Let me ask if the following is a condition or a restriction: We have no evidence of what evolution or proteins would be like on another planet. We assume that it will be very different, but that's a guess. Not even an educated guess. So there's really nothing to say that proteins aren't related in the form of there's really only one way life can be expressed at that level. So... is it a condition that evolution on other planets must be incompatible despite having same-shape proteins? Or is it acceptable that evolution on other planets is compatible? $\endgroup$
    – JBH
    Jul 5, 2023 at 1:18
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    $\begingroup$ This is related to one of the "unsolved" problems in biology, that of the complexities of protein folding. Getting an actual legitimate answer (especially considering that we're still stuck here on Earth alone) is going to be next to impossible. I'd advise reading around the topic and fudge it best you can. (Remembering that certain fold configurations are more energetically favourable than others and thus more likely to be common, but not necessarily. Selection came up with peacock tails after all). $\endgroup$ Jul 5, 2023 at 1:53
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    $\begingroup$ The sentence "protein shapes that perform the same function are highly conserved across species, even those not related" is not well formed. If the two species are not related there is nothing to conserve. When we say that a gene or a protein is (highly or not not) conserved, we mean that it has not changed much from the most recent common ancestor. If there is no common ancestor, the concept of conservation does not apply. (And anyway, there is no way for proteins made of different amino-acids to have the exact same shape.) $\endgroup$
    – AlexP
    Jul 5, 2023 at 3:10
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    $\begingroup$ @inkwell87 We don't know. That's the problem of having only one data point (Earth). Everything else is speculation - but that's where worldbuilding comes into play. You're setting the rules. If you want what you're asking for, there's nothing to say it's wrong to draw a line at the complexity of DNA claiming that "scientists discovered to their delight that the fundamentals of life are the same everywhere." At that point you can believably (to all but a specialist in the field... do we care about that?) set your protein rule and move on. $\endgroup$
    – JBH
    Jul 5, 2023 at 16:03
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    $\begingroup$ It isn't enough to have the same shape. The proteins have to have the same atoms at the same places in order to have the same function. It is far more likely to have slightly different shapes and slightly different functions because the collection of proteins have to work together to make an organism live. $\endgroup$
    – David R
    Jul 6, 2023 at 14:00

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Nothing. There is nothing that would cause protein shapes to be the same across urelated species.

Even here on Earth you can have completely different proteins with completely different shapes having the same function. True, there can be similarities in form when doing the same job with the same mechanism, but biology can often do same thing with different mechanisms. And it is higly unlikely a different biochemistry with different amino-acid analogues will use exactly same mechanisms to do something. Even if the environment would be identical to Earth. And every change in the environment increase the odds of divergence.

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    $\begingroup$ There are several examples on earth of unrelated organisms which all produce proteins with similar structural motifs despite the coding DNA sequence being completely different. Of course, it's more difficult on a completely different planet, but the premise that unrelated species can't have related protein shapes is false. See humgenomics.biomedcentral.com/articles/10.1186/1479-7364-6-10 $\endgroup$ Jul 7, 2023 at 16:31
  • $\begingroup$ @NuclearHoagie And jet those "unrelated" organisms (there is no such thing on Earth) still use identical nucleotides, identical aminoacids, and importantly, have extremely similar processes. Your article has several examples of DNA-binding proteins. It is natural that some protein shapes will be similar as there are only so many ways for a protein to bind to a DNA. $\endgroup$
    – Negdo
    Jul 11, 2023 at 6:34
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What would cause proteins to be the same shape? The laws of chemistry and the same goal. Protein shapes are the function. In natural biology shapes are conserved more than actual amino acid sequences. But when other planets get involved there may be other shapes that work good enough. Point being evolving something that will work a little bit probably isn't as near impossible as some would say - and when something works a little evolution can rapidly make it work a lot better. Also proteins are modular (called motifs).

I'd personally speculate things like alpha helixes will show up on any planet using amino acids.

Something like molecular chlorophyll will probably use the same basic chemistry and have a little variety. But a peridinin-chlorophyll-protein complex will have a lot of alternate solutions with similar functions in other biologies.

We are at the dawn of computers being able to predict structures accurately. For example this experiment used AI to design a protein with a goal function - and the sequence was quite different than known natural sequences.

https://news.mit.edu/2023/ai-system-can-generate-novel-proteins-structural-design-0420

Realistic yet novel designs

"They tested their models by comparing the new proteins to known proteins that have similar structural properties. Many had some overlap with existing amino acid sequences, about 50 to 60 percent in most cases, but also some entirely new sequences. The level of similarity suggests that many of the generated proteins are synthesizable, Buehler adds."

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    $\begingroup$ I think this is pretty misleading. Evolution and chemistry do not have any specific goal. Even then, having the same goal dosnt even remotely mean evolution would end up "choosing" the same shape across unrelated species. $\endgroup$
    – ErikHall
    Jul 7, 2023 at 9:39
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A Progenitor Race... You don't want any Shared Evolutionary History, so let's throw out the evolutionary part of all planet's shared history with respect to intelligent life. Maybe in your universe, there was a Progenitor Race which visited all of the planets where intelligent life now flourishes. Maybe those genetic engineer's seeded life across the galaxy, building it a little different each time, but always adhering to some basic design elements.

  • Why are so many species built of similarly shaped proteins? Because those are the shapes which the Progenitors knew would work.

  • Why are those shapes implemented differently on each different planet? Because doing things the same way every time is boring and the Progenitors enjoyed the challenge of diversity for artistic reasons.

They also could have been changing the recipe on every planet because another ancient race (the anti-progenitors) were launching progressively more advanced pathogens at the each planet they successfully seeded, basing each bio-attack on samples taken from the previous planet. Each planet had to be different or the anti-progenitors' current viral arsenal would wipe out everything the progenitors had planted.

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