Stellaris Dev Diary #379 - You Are What You Eat

[Katzui]

Stitch

 

[cryptkeeper]

We're also looking at removing the technologies from the Genetics tree in Utopia - if you have the tradition that should be enough to get the traits

Does this mean we will get the trait just from killing the leviathans or no leviathans required ? I hope the first one and not the latter, as it was interesting to have to put work in to get those traits.

 

[Tannhäuser Cake]

Does this mean we will get the trait just from killing the leviathans or no leviathans required ? I hope the first one and not the latter, as it was interesting to have to put work in to get those traits.

Perhaps it could be a technology that is gained from (the corpse of) the leviathan? It could then be stolen by someone else, who would then also gain the ability to use the trait (provided their understanding of genetics is sufficient?).

 

[Ajacoba]

Perhaps it could be a technology that is gained from (the corpse of) the leviathan? It could then be stolen by someone else, who would then also gain the ability to use the trait (provided their understanding of genetics is sufficient?).

Why are you people confused about this?
It's gonna be the exact same thing as with the machine empires
Kill the leviathan, integrate it into your main species

 

[T5_k]

Why are you people confused about this?
It's gonna be the exact same thing as with the machine empires
Kill the leviathan, integrate it into your main species

Yeah, it is pretty clearly written. Like, no leviathans mentioned anywhere, at least not in the dev diary.
I guess they got confused by this post?

Seems like it
The final mutation mentions both phenotype genes and leviathans

since in it leviathans are mentioned, but I have 0 clue where this poster got leviathans from.


It's pretty safe to assume you'll still need to kill leviathans (along with choosing the correct situation approach) to get leviathan traits.

 

[Tannhäuser Cake]

Why are you people confused about this?
It's gonna be the exact same thing as with the machine empires
Kill the leviathan, integrate it into your main species

No idea what "people" you are talking about, and I am not confused. You are reading more into my post than is there; I just wrote a reply elaborating hypotetically on what was in the text I quoted, nothing more.

 

[Connacht]

Please do not use "genetic code" as a synonym of "genome".

 

[grommile]

Please do not use "genetic code" as a synonym of "genome".

I assume this is more than aesthetic bikeshedding, so would you care to clarify?

 

[stilgarpl]

I assume this is more than aesthetic bikeshedding, so would you care to clarify?

It's like calling a book "the alphabet".

 

[Connacht]

I assume this is more than aesthetic bikeshedding, so would you care to clarify?

In short, the genetic code is a set of "instructions" by which the sequences of those molecules called nucleotides that compose DNA (and RNA) are "translated" into aminoacids, and thus proteins. It is not some kind of "list of traits" that a species possesses into its DNA, despite many people mistakenly refer to the sum of our genes as the "genetic code".

It is a bit like having a set of characters in a printing press, there are rules by which you arrange them to form words (genetic code), but it is not the manuscript with pages and chapters (genome). So you cannot "add a trait" to the genetic code like suggested here:

You can add/modify a gene into a genome, for example you take from a particular jellyfish the gene that codes for the synthesis of a fluorescent protein, and add it to a bacterium (or a cat!) to get nice green fluo beings. This is the equivalent of adding traits to a species, like adding a new word into a vocabulary.

I won't deal with the accuracy of considering complex anatomic features as if they were pieces to assemble (there isn't really a "gene for wings" but the genetic control of embryonal development is much more complex), since it would be excessive nitpicking for a space fantasy game. But the more correct terminology can and should be pointed out. Kinda similar to how the first versions of Stellaris incorrectly used pre-sentient instead of pre-sapient.

 

[grommile]

In short, the genetic code is a set of "instructions" by which the sequences of those molecules called nucleotides that compose DNA (and RNA) are "translated" into aminoacids, and thus proteins. It is not some kind of "list of traits" that a species possesses into its DNA, despite many people mistakenly refer to the sum of our genes as the "genetic code".

In the same way that I, a computer programmer, refer to the instructions by which a computer rearranges bits in its memory and toggles signal lines in order to produce beautiful moving pictures as "machine code", then?

(And the human readable version of those instructions as "source code".)

 

[Connacht]

In the same way that I, a computer programmer, refer to the instructions by which a computer rearranges bits in its memory and toggles signal lines in order to produce beautiful moving pictures as "machine code", then?

(And the human readable version of those instructions as "source code".)

DNA is composed by sequences of organic molecules called nucleotides, of which it has four types, identified by the letters A, T, C, G (in RNA we have U that replaces T and it is functionally equivalent).

Inside the cell there are several other specialized molecules that can chemically recognize and "read" those letters, to "convert" them into a corresponding aminoacid (plus a few exceptions for other related functions). They do that by reading nucleotides in groups of three, which are first "transcribed" into a small RNA strand, which is then "translated" into the aminoacid.

So, for example, the sequence GGG, which codes for an aminoacid called glycine, the simplest of all. This is the genetic code, in essence.

When you have several of these triplet sequences, in the end you get a chain of aminoacids. More complex assemblages form proteins, ranging from the structural ones that build up your muscles to the enzymes that regulate your metabolism. Genes are sequences of nucleotides that code for something.

For example our body produces a very short and simple compound called glutathione, which is composed by the aminoacids glutammate, cysteine, and glycine. They correspond to the sequences GAG, UGC, GGG; what you find would be the string GAGUGCGGG that acts as a template for the assembly of the correct aminoacids.

If you remember the film GATTACA, its title was referring to this.

The genetic code is not the sum of all the genes (DNA sequences) that control our traits. The genetic code is the fact that when you have a sequence of three letters inside a gene, they will be translated into certain aminoacids, regardless of what in the end will turn out from that gene.

With a few little exceptions, all codes are conserved across all living beings on Earth, hinting that they evolved a long time ago in a single organism from which we all descend, and that changes in how this works would likely be unoptimal/fatal for us.

EDIT: typos

 

[Tseudonym]

Although, since the sequence of nucleotides encodes genetic information, one could colloquially call it a code in the sense of "cypher or encryption"

 

[Newbee53]

In short, the genetic code is a set of "instructions" by which the sequences of those molecules called nucleotides that compose DNA (and RNA) are "translated" into aminoacids, and thus proteins. It is not some kind of "list of traits" that a species possesses into its DNA, despite many people mistakenly refer to the sum of our genes as the "genetic code".

It is a bit like having a set of characters in a printing press, there are rules by which you arrange them to form words (genetic code), but it is not the manuscript with pages and chapters (genome). So you cannot "add a trait" to the genetic code like suggested here:

View attachment 1282400

You can add/modify a gene into a genome, for example you take from a particular jellyfish the gene that codes for the synthesis of a fluorescent protein, and add it to a bacterium (or a cat!) to get nice green fluo beings. This is the equivalent of adding traits to a species, like adding a new word into a vocabulary.

I won't deal with the accuracy of considering complex anatomic features as if they were pieces to assemble (there isn't really a "gene for wings" but the genetic control of embryonal development is much more complex), since it would be excessive nitpicking for a space fantasy game. But the more correct terminology can and should be pointed out. Kinda similar to how the first versions of Stellaris incorrectly used pre-sentient instead of pre-sapient.

DNA is composed by sequences of organic molecules called nucleotides, of which it has four types, identified by the letters A, T, C, G (in RNA we have U that replaces T and it is functionally equivalent).

Inside the cell there are several other specialized molecules that can chemically recognize and "read" those letters, to "convert" them into a corresponding aminoacid (plus a few exceptions for other related functions). They do that by reading nucleotides in groups of three, which are first "transcribed" into a small RNA strand, which is then "translated" into the aminoacid.

So, for example, the sequence GGG, which codes for an aminoacid called glycine, the simplest of all. This is the genetic code, in essence.

When you have several of these triplet sequences, in the end you get a chain of aminoacids. More complex assemblages form proteins, ranging from the structural ones that build up your muscles to the enzymes that regulate your metabolism. Genes are sequences of nucleotides that code for something.

For example our body produces a very short and simple compound called glutathione, which is composed by the aminoacids glutammate, cysteine, and glycine. They correspond to the sequences GAG, UGC, GGG; what you find would be the string GAGUGCGGG that acts as a template for the assembly of the correct aminoacids.

If you remember the film GATTACA, its title was referring to this.

The genetic code is not the sum of all the genes (DNA sequences) that control our traits. The genetic code is the fact that when you have a sequence of three letters inside a gene, they will be translated into certain aminoacids, regardless of what in the end will turn out from that gene.

With a few little exceptions, all codes are conserved across all living beings on Earth, hinting that they evolved a long time ago in a single organism from which we all descend, and that changes in how this works would likely be unoptimal/fatal for us.

EDIT: typos

While I can't remember enough to find it on google in the handful of minutes I have, I'm pretty sure there is one rare clade of microorganisms that uses a different code for stop. because there are 'stop' and 'start' codes as well, to tell the cells what parts of the DNA is to be used and where one starts making said copies for use. And stops as well. this means that one cannot assume that aliens who somehow use DNA will use the same codes for everything we earth based life will use it for.

However, SiFi has run on lego genetics for so long that it would honestly be kind of off putting if stellaris didn't.

 

[DreadLindwyrm]

While I can't remember enough to find it on google in the handful of minutes I have, I'm pretty sure there is one rare clade of microorganisms that uses a different code for stop. because there are 'stop' and 'start' codes as well, to tell the cells what parts of the DNA is to be used and where one starts making said copies for use. And stops as well. this means that one cannot assume that aliens who somehow use DNA will use the same codes for everything we earth based life will use it for.

However, SiFi has run on lego genetics for so long that it would honestly be kind of off putting if stellaris didn't.

There are three standard stop codons, and another bunch of known ones. https://en.wikipedia.org/wiki/Stop_codon
Vertebrates apparently break the "standard" 3, and have their own couple of additional ones.

Apparently we get a few start codons as well https://en.wikipedia.org/wiki/Start_codon#Alternative_start_codons So some of them might need to be "read" conditionally.

 

[Abdulijubjub]

While I can't remember enough to find it on google in the handful of minutes I have, I'm pretty sure there is one rare clade of microorganisms that uses a different code for stop. because there are 'stop' and 'start' codes as well, to tell the cells what parts of the DNA is to be used and where one starts making said copies for use. And stops as well. this means that one cannot assume that aliens who somehow use DNA will use the same codes for everything we earth based life will use it for.

However, SiFi has run on lego genetics for so long that it would honestly be kind of off putting if stellaris didn't.

It much more than just "cannot assume [it's the same]". It's "it would be insane to even consider it might be the same".

Even the idea that life forms from a different biosphere would use exactly the molecules to serve the purpose of DNA, or even proteins, is sketchy.

And, if they did, that the same codes correspond to the same amino acids and thus produce the same proteins is completely unbelievable: there are 4^3=64 possible nucleotide combinations, and 21 things to code for (including Stop). That means there are billions of different equally valid mappings, even after accounting for things like UC* all mapping to Serinine (which makes clustering energetically preferable, and drops some of them from being approximated by 64 choose 21 to roughly 40 choose 21).

The idea that genes from different xenos would be even remotely compatible (even for making the same proteins, much less coding for e.g. responses to hormone gradients and cell specialization that determine the development of something as complex as a limb) is completely implausible.

But, as you say, it's more fun to assume that it would be, so SciFi (generally) assumes it is. Which makes all the "it's unrealistic to assume you can just take a trait from genes" thing a bit trite: we're way, way past that into the realm of utterly-implausible-but-fun-to-imagine. May as well go all the way.

 

[zombiezome1444]

Do presapients count as unique species in your empire for situation progress? I have in my head the idea of a genesis guides build that makes a bunch of presapients, and doing a hive mind version, but if I need to uplift them it would be sad because it would take longer for the hive mind version to get off the ground because I wouldn't want to kill them I'd want to have them stay and be my friends in evolution.

Edit: Also I feel like everyone above me is discounting the idea of convergent evolution and the fact that if a protein is good enough at its job multiple carbon based lifeforms might just repeatedly use similar proteins to perform similar functions. Direct DNA compatibility on the other hand I agree is pretty far fetched, but the idea of having a deep enough understanding of things to replicate traits isn't implausible.

Edit 2: I could also just turn them to livestock...

 

[Tseudonym]

It much more than just "cannot assume [it's the same]". It's "it would be insane to even consider it might be the same".

Even the idea that life forms from a different biosphere would use exactly the molecules to serve the purpose of DNA, or even proteins, is sketchy.

There is a certain extent where alien life would be expected to use the same molecules simply because they are the only molecules that can perform the chemical reactions necessary to achieve the desired function. For example, nucleic acids are the only know molecules capable of encoding genetic information (You could theoretically translate a protein in reverse, but this has not been observed in nature, and you're still translating into a nucleic acid anyway). Most biologists expect extraterrestrial life, if it exists, to use much of the same baseline as what is used on Earth, even if it's not 100% identical.

 

[Tseudonym]

While I can't remember enough to find it on google in the handful of minutes I have, I'm pretty sure there is one rare clade of microorganisms that uses a different code for stop. because there are 'stop' and 'start' codes as well, to tell the cells what parts of the DNA is to be used and where one starts making said copies for use. And stops as well.

There are three standard stop codons, and another bunch of known ones. https://en.wikipedia.org/wiki/Stop_codon
Vertebrates apparently break the "standard" 3, and have their own couple of additional ones.

Apparently we get a few start codons as well https://en.wikipedia.org/wiki/Start_codon#Alternative_start_codons So some of them might need to be "read" conditionally.

This reminds me of an interesting system that exists in our own DNA. Human DNA only codes for 20 amino acids, but the are 21 standard amino acids used by the human body in protein synthesis. The is a specific sequence of nucleotides that does not code for anything, but it's presence causes a following UGA codon (a stop) to instead code for the 21st amino acid, selenocysteine.

 

[Abdulijubjub]

There is a certain extent where alien life would be expected to use the same molecules simply because are the only molecules that can perform the chemical reactions necessary to achieve the desired function. For example, nucleic acids are the only know molecules capable of encoding genetic information (You could theoretically translate a protein in reverse, but this has not been observed in nature, and you're still translating into a nucleic acid anyway). Most biologists expect extraterrestrial life, if it exists, to use much of the same baseline as what is used on Earth, even if it's not 100% identical.

That one is plausible. But it's definitely not true that nucleic acids are the only molecules that could serve that purpose. They may be the only ones we know that are used, but their properties aren't that selective. Even to make something exactly like DNA (which is not the only possible way to store sequential information in organic molecules), you just need a polymer and something which can attach to the sides of that polymer/form pairs with another similar molecule (for stability, though some things, like viruses, get by with just RNA).

We even have two competing versions of such a system: RNA and DNA. And they don't even use the same 4 nucleic acids: uracil and thymine swap from one to the other. DNA's nucleic acids aren't even the only ones that can store information that way on Earth.

Some things will be identical. Sugar is one: it's just a great simple monomer/polymer that can be used for everything from energy storage to structural members; it's likely that it would get used. But amino acids aren't. We don't even have the same amino acids in all forms of life on earth: Pyrrolysine is seemingly unique to Archaea.

Amino acids are a bunch of weird monomers with lots of different shapes and hydrogen bonding sites that mean they can be folded to make a complex 3d shapes despite being assembled sequentially into polymers. And you could do similar things with lots of other sets of building blocks, though computing exactly how to do it with any set is computationally intractable (protein folding problem with zero training data and no guarantee that any given set is actually valid for a purpose) so we're not likely to see a reproduction any time soon.

But it's plausible that you could make protein-like structures out of lots of things, at least as far as I'm aware.

-----

Biologists assume (rationally) that it will use the same building blocks, or something similar, because we have nothing else to go on and speculating about some unknown biochemistry is unhelpful at best; better to assume it's roughly the same as what we have and work from there.

And it really could use almost identical molecules: there are more things than just sugar that are used because they're very energetically favorable and just the best fit. It would be convergent evolution (on the biosphere level). That's why I described that part (using exactly the same molecules) as "sketchy", not impossible.

But using exactly the same genetic code is basically inconceivable. And using exactly the same hormones to do the same signaling to develop the same cell types during limb or organ development is another level of inconceivable on top of that.