4 ms·

> Like, why didn't DNA end up as base 3? Why did we end up with only 20 proteinogenic amino acids? Why are vertebrate neural architectures inverted (cell bodi

> Like, why didn't DNA end up as base 3? 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.

sparrowInHand 3y ago
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.
t_serpico 3y ago
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 https://arxiv.org/pdf/q-bio/0605036.pdf for interesting thoughts. Remember, evolutionary biology is a field and people think about these questions!
- idiotsecant 3y ago
  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.
  - hotstickyballs 3y ago
    If you iron man the argument then it’s an error correction argument in that this simple ecc method can be what favours a base-4 encoding instead
  - t_serpico 3y ago
    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.pdf https://www.math.unl.edu/~bdeng1/Papers/DengDNAreplication.p... for what seems to be an interesting analysis regarding base number and DNA replication rate.
    - usrbinbash 3y ago
      > 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.
      - 3y ago
function_seven 3y ago
> (eg. our light sensitive cells point in the wrong direction) Can you expand on that? Are you talking about front-facing eyes vs. birds' eyes? Or something else like retinal structure?
- dtgriscom 3y ago
  Retinal structure: https://en.wikipedia.org/wiki/Retina#Inverted_versus_non-inverted_retina https://en.wikipedia.org/wiki/Retina#Inverted_versus_non-inv...
- metabagel 3y ago
  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. https://en.wikipedia.org/wiki/Retina#/media/File:Retina-diagram.svg https://en.wikipedia.org/wiki/Retina#/media/File:Retina-diag... Edit: ninja'd
  - dekhn 3y ago
    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.
    - usrbinbash 3y ago
      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.
erenyeager 3y ago
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.

sparrowInHand 3y ago

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.

t_serpico 3y ago

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 https://arxiv.org/pdf/q-bio/0605036.pdf for interesting thoughts. Remember, evolutionary biology is a field and people think about these questions!

idiotsecant 3y ago
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.
- hotstickyballs 3y ago
  If you iron man the argument then it’s an error correction argument in that this simple ecc method can be what favours a base-4 encoding instead
- t_serpico 3y ago
  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.pdf https://www.math.unl.edu/~bdeng1/Papers/DengDNAreplication.p... for what seems to be an interesting analysis regarding base number and DNA replication rate.
  - usrbinbash 3y ago
    > 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.
    - 3y ago

function_seven 3y ago

> (eg. our light sensitive cells point in the wrong direction) Can you expand on that? Are you talking about front-facing eyes vs. birds' eyes? Or something else like retinal structure?

dtgriscom 3y ago
Retinal structure: https://en.wikipedia.org/wiki/Retina#Inverted_versus_non-inverted_retina https://en.wikipedia.org/wiki/Retina#Inverted_versus_non-inv...
metabagel 3y ago
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. https://en.wikipedia.org/wiki/Retina#/media/File:Retina-diagram.svg https://en.wikipedia.org/wiki/Retina#/media/File:Retina-diag... Edit: ninja'd
- dekhn 3y ago
  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.
  - usrbinbash 3y ago
    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.

erenyeager 3y ago

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.