Why did we end up with only 20 proteinogenic amino acids? Why are vertebrate neural architectures inverted (cell bodies on the inside, connections on the outside, even though the other way round way (eg. like a squids brain is organised) is easier and less inhibitive to growth?
2 Reasons:
a) Because nature and evolution cannot engineer. Random mutation, recombination and natural selection are the only mechanisms available. Things get selected if they outcompete existing alternatives, they don't need to be the best solutions.
b) All solutions have to be built by modifying what already exists. Evolution doesn't get to do greenfield projects, because anything that has to start from scratch is so disadvantaged in natural selection compared to already evolved complex life, it will fail.
This leads to systems that, from an engineering point of view, don't always make a lot of sense.
Eg. the architecture of the vertebrate neural system creates a lot of issues (eg. our light sensitive cells point in the wrong direction). The only way this makes any sense if when one looks at how the neural tube (the precursor to the backbone) is formed by the endodermis folding in on itself. This process is so deeply at the root of the Chordata, and so many other things depend on it, that it simply cannot change any more.
Many many biological systems are "legacy systems" in the truest sense of the word: Solutions produced a long time ago that may have many problems, but are simply too deeply enmeshed with everything that came after, that they are now impossible to change.
A classic armchair response. DNA has complementary nucleotides (AT,GC) that facilitates its pairing. Base 3 wouldn’t work in that sense. Also, you can’t forget about the genetic code. See https://arxiv.org/pdf/q-bio/0605036.pdf for interesting thoughts. Remember, evolutionary biology is a field and people think about these questions!
This is pretty smug for someone who seems to have managed to miss the point entirely. Yes, DNA has certain features that require a base 4 system. That is not necessarily true of all possible systems with DNA-equivalent function, which is the point this whole thread is making.
How have I missed the point? The answer that nature cannot engineer and can't start de novo are trivially true statements that provide no actual insight into the question. I fully agree the original question itself is a deep one. A quick literature search is more productive than pontificating with weak analogies. See https://www.math.unl.edu/~bdeng1/Papers/DengDNAreplication.p... for what seems to be an interesting analysis regarding base number and DNA replication rate.
> that provide no actual insight into the question
Mind elaborating on that?
Because there is no biochemical reason why DNA could not have incorporated, say, a third pairing pair, so while base-3 (which I don't specifically mention in my post btw.) wouldn't work, base 6 or 8 would have been possible. "Unnatural Base Pairs" are even known to work in laboratory settings.
There is also no biochemical reason why base2 life wouldn't work. Expand the reading frame of the translation machinery to 5 instead of three, and you have enough coding space for polypeptides.
My answer adresses the question completely, because the only reason behind these "decisions" is an ancient system that simply got "frozen", and now cannot change any more.
> There is also no biochemical reason why base2 life wouldn't work.
are you sure about that? are you sure there's no weird effects that might destabilize very long sequences of 2-nucleotide DNA? or on how wide DNA-binding domains have to be to cope with reduced information density, and how that might sterically hinder smaller arrangements of proteins?
> My answer adresses the question completely, because the only reason behind these "decisions" is an ancient system that simply got "frozen", and now cannot change any more.
your answer is just a hypothesis, not a proof. these things can be studied (by studying abiogenesis in-vitro), and it's not certain these decisions were "flash frozen" like you describe. 2-, 4-, and 6- nucleotide coding systems might have coexisted in the RNA world, and 4- could have won out for some reason.
Yes, I am sure about that, because I used to study Biology before going into IT. And we had a lovely lecture in which we used to discuss theoretical setups for lifeforms at a molecular level.
2 nucleotide DNA isn't necessarily less stable. AT-rich domains have less bindings, but if stablity is the issue, use CG instead (3 bindings)...although that is also a compromise, because then opening DNA for transcription gets more difficult.
> your answer is just a hypothesis, not a proof.
My answer is what we observe in evolutionary biology.
I have given an example outside of the molecular world for a reason. There is no real advantage to the inversion of the neural architecture in Chordata, it just didn't matter when the neural tube formation mechanisms came to be. Now, with mammals having huge brains and complex sensory organs, the warts in that design show.
The proof for that is easy to come by, (also a reason btw. why the neural inversion is my favorite example for this): Look an any Protostomia. Their neural system isn't inverted. Consequently, Squids don't have a visual blind spot.
your example of the blind spot is quite elegant and convincing. I think it's partly so convincing because there's a large fossil record and diverse phylogenetic tree, with many gaps covered. conversely, we're missing direct evidence for the pre-LUCA era, and what we have is bottlenecked. this makes me more skeptical.
for instance, I've seen arguments that the codon mapping, and even the particular set of protein- coding amino acids, that we ended up with was arbitrary, but I've also read papers arguing that the amino acids include a sort of spanning set of different structural scaffolds with different polarity that happen to mesh well with DNA, and that the particular choices of codons were influenced by how the RNA t-acyl transferases arose, etc.
so, I'm still unconvinced, but I find this area fascinating to read about.
Idk enough about this discussion to argue it, but his hypothesis does not imply your second point couldn't be true.
> your answer is just a hypothesis, not a proof. these things can be studied (by studying abiogenesis in-vitro), and it's not certain these decisions were "flash frozen" like you describe. 2-, 4-, and 6- nucleotide coding systems might have coexisted in the RNA world, and 4- could have won out for some reason.
His hypothesis is, at least in part, “4- won for some reasons for which we have no explanation, and it stayed that way for some reason [that we may or may not know].” I suppose the reason would be that 4- was somehow better suited for the particular use-case at the time.
Of course there’s a ton of interesting details to discuss to discover, and whether if multiple systems coexisted is one of many fascinating things to discuss, and his response never said otherwise.
Short answer: Likelihood of noise (brownian motion) producing the element and keeping it interacting. Then once it gets going, likelihood of keeping state, while interacting.
Lefthand is a vertebrate eye, righthand is a squids eye.
In Vertebrates (really in all Chordata), the light sensitive "tips" of the sensory cells point inwards, aka. the exact wrong direction. At the base of the cells are the axons (nerve connections) which transmit the information into the brain.
Due to the aforementioned orientation, these axons run along the outer layer of our light sensitive cells, and at some point have to travel "invards" towards the brain. At that point there can be no cell bodies, and that's the "visual blind spot" of our eyes.
A squids eye doesn't have that problem; all the light sensitive cells point outwards, the axons are at the innermost layer, and connectivity can be achieved without a blind spot (also, they don't need a reflective layer).
I had to look this up, and I guess what usrbinbash was referring to was the layout of the retina, which places the rods and cones behind layers of transparent neurons.
Yet, it doesn't really have a strong impact as it's been determined that humans can see individual photons and we aren't dependant on night vision for hunting.
It doesn't have a strong impact, and the design also doesn't prevent good night vision (the basic structure of a cats eye is similiar, ALL chordata have an inverted neural makeup).
But that doesn't mean the setup makes sense, and that is exactly my point.
And long term, this has an impact. For example, vertebrate brain size is limited by the simple factor, that we have to put all the connections on the outside. The more neuronal bodies we have, the more connections they require.
N <---> N
In this clumsy diagram, 2 neurons talk with the connections on the inside. However, vertebrate brains have to do this instead:
+--------------+
| |
+-> N N <-+
It's easy to see how the second setup becomes prohibitive when more Neurons are added to it. The brains of Protostomia again don't have that problem...they can have the connections on the inside, and the neuron bodies on the outside, aka. the logical setup.
Now there are ways around that, eg. Reptile and Bird brains grow in bulbs that theoretically allow sustained growth without the connective layer getting in the way. But similar to the reflective layer in our eyes, this is not a setup that's there because it makes a lot of sense...it's a hack, a workaround for some "legacy system", that is now so enmeshed, it's impossible to change.
It’s a bit anthropocentric to talk about not making sense from an engineering point of view. One example is the recurrent laryngeal nerve which always appears to take unnecessary detours to people because of what is thought to be historical evolution. But there is deep wisdom and insight we have gleaned in this, but I think it’s not for us to say well we could engineer this better, we don’t have the total knowledge of tools yet & it is dismissive and say disrespectful of the wondrous biological systems that have been made to sustain life.
Hubris and attempts to alter inherent nature are often tied up ironically. But we can benefit a lot more from biological humility, realizing there are many unknown unknowns.
Why did we end up with only 20 proteinogenic amino acids? Why are vertebrate neural architectures inverted (cell bodies on the inside, connections on the outside, even though the other way round way (eg. like a squids brain is organised) is easier and less inhibitive to growth?
2 Reasons:
a) Because nature and evolution cannot engineer. Random mutation, recombination and natural selection are the only mechanisms available. Things get selected if they outcompete existing alternatives, they don't need to be the best solutions.
b) All solutions have to be built by modifying what already exists. Evolution doesn't get to do greenfield projects, because anything that has to start from scratch is so disadvantaged in natural selection compared to already evolved complex life, it will fail.
This leads to systems that, from an engineering point of view, don't always make a lot of sense.
Eg. the architecture of the vertebrate neural system creates a lot of issues (eg. our light sensitive cells point in the wrong direction). The only way this makes any sense if when one looks at how the neural tube (the precursor to the backbone) is formed by the endodermis folding in on itself. This process is so deeply at the root of the Chordata, and so many other things depend on it, that it simply cannot change any more.
Many many biological systems are "legacy systems" in the truest sense of the word: Solutions produced a long time ago that may have many problems, but are simply too deeply enmeshed with everything that came after, that they are now impossible to change.