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Tl;dr Biology is applied chemistry, chemistry is applied quantum physics and in some cases chemistry is a leaky abstraction and does not perfectly explain what

by danbruc 10y ago

Tl;dr Biology is applied chemistry, chemistry is applied quantum physics and in some cases chemistry is a leaky abstraction and does not perfectly explain what is going on in organisms. Three examples - photosynthesis being more efficient than expected, birds sensing Earth's magnetic field by an unknown mechanism and a lack of understanding how olfaction works in detail - are presented but besides that there are no new revolutionary ideas in the article.

kakarot 10y ago
I was under the assumption that the working theory is birds share a similar feature as fruit flies and possibly foxes. The cones that allow us to see blue light actually work as compasses when suspended in a fluid, and they are not attached to the retina of a fruit fly but are suspended in their eye and thus shape incoming visual patterns around magnetic fields https://en.wikipedia.org/wiki/Magnetoreception https://en.wikipedia.org/wiki/Magnetoreception
- Aelinsaar 10y ago
  That's fascinating, but birds do have their rods and cones attached to the retina. IIRC birds are though to be in some way detecting either directly, or through secondary effect, polarization of light.
- danbruc 10y ago
  That is essentially the proposed mechanism discussed in the article but the article gives the impression - at least to me - that it is not yet confirmed that this indeed how it works in birds. EDIT: After skimming the Wikipedia article, both articles agree that it is a possible but not yet confirmed mechanism.
- dnautics 10y ago
  The cryptochrome hypothesis doesn't require detachment from the retina as it's a protein that has directional excitatory preference, not the whole cell.
  - kakarot 10y ago
    Interesting. Thanks for the clarification. I find this topic to be of extreme interest
fizixer 10y ago
> ... chemistry is a leaky abstraction ... Well I second you on that. Even stronger: All of (theoretical) science is a leaky abstraction. When an area is new, people are doing the spherical-cow-approximation willy nilly. After it gets established, corner cases start to surface. Incidentally, theoretical physicists are the masters of creating spherical-cow-approximations and leaky-abstractions. They're always going for the next big unexplored territory. E.g., once QM got established as a theory, they moved on to high-energy, while there is about 1000x more work to be done picking up the pieces of QM in the areas of solid-state-physics and molecular-chemistry. (largely speaking that is; not everyone is like that).
- sriku 10y ago
  A meta spherical cow?
- jp3141 10y ago
  relevant xkcd https://www.xkcd.com/435/ https://www.xkcd.com/435/
  - Noseshine 10y ago
    Math is a tool. It's orthogonal and used by all, not hierarchical above (or below) all of them.. http://euclid.trentu.ca/math/sb/misc/mathsci.html http://euclid.trentu.ca/math/sb/misc/mathsci.html > The natural sciences investigate the physical universe but mathematics does not, > so mathematics is not really a natural science. This leaves open the subtler > question of whether mathematics is essentially similar in method to the natural > sciences in spite of the difference in subject matter. I do not think it is. I'm not even including that famous Einstein quote about math. Example: When you are doing math in economics you are not doing something that is even more foundational than physics.
    - rpwverheij 10y ago
      what if the nature of the physical universe has no other reason to be as it is other than mathematical consequences of harmonies, resonances, balances, etc? In other words: if all that exists follows mathematical law, doesnt that make math part of the existential?
sriku 10y ago
Good summary. Classical physics is not good enough for chemistry. So why are we surprised that without a quantum foundation, biology cannot function at all? OTOH, we have a theory that classical computation adequately accounts for intelligence. Finding an unavoidable quantum route that nature has picked would certainly be interesting, despite that quantum Turing machines are also classically computable (I think).
- eli_gottlieb 10y ago
  >OTOH, we have a theory that classical computation adequately accounts for intelligence. Finding an unavoidable quantum route that nature has picked would certainly be interesting, despite that quantum Turing machines are also classically computable (I think). I don't think we have a foundation for classical computation without thermodynamics, which is a classical theory whose ultimate foundations probably require quantum information theory.
nabla9 10y ago
>in some cases chemistry is a leaky abstraction There has never been "classical" theory for chemistry like there has been classical mechanics that works reasonably well within limits, just weird heuristic rules. Chemistry is quantum chemistry is quantum electrodynamics.
Gatsky 10y ago
Can you provide an example of how this rather facile assertion leads to any insight into biology? For example, how does it follow in a coherent fashion that the chemical properties of DNA lead to Mozart, or a lady bug? In short, how does chemistry explain either the origin, function or future trajectories of any of the utterly amazing biological entities that exist today?
- kenbellows 10y ago
  I mean... evolution explains the complexity of things, and evolution certainly has a foundation in the chemistry of DNA. Or are you asking why we have the particular configuration of biological entities we have instead of a different one?
  - Gatsky 10y ago
    Well what does it mean to say that Biology is applied Chemistry? To me it says 2 things. 1 - That there is no 'new' knowledge in biology. 2 - The important aspects of biology can be reduced easily to applied chemistry. Evolution contradicts this, because it is a genuinely new idea. Some may say it is the ONLY new idea in biology, but that's good enough. It's often quoted here that "Computer Science is no more about computers than astronomy is about telescopes." You could extend this to "Biological science is no more about chemistry..."
anotheryou 10y ago
Or: If it can be optimized/exploited by evolution, of course it will be.

by danbruc 10y ago

kakarot 10y ago

I was under the assumption that the working theory is birds share a similar feature as fruit flies and possibly foxes. The cones that allow us to see blue light actually work as compasses when suspended in a fluid, and they are not attached to the retina of a fruit fly but are suspended in their eye and thus shape incoming visual patterns around magnetic fields https://en.wikipedia.org/wiki/Magnetoreception https://en.wikipedia.org/wiki/Magnetoreception

Aelinsaar 10y ago
That's fascinating, but birds do have their rods and cones attached to the retina. IIRC birds are though to be in some way detecting either directly, or through secondary effect, polarization of light.
danbruc 10y ago
That is essentially the proposed mechanism discussed in the article but the article gives the impression - at least to me - that it is not yet confirmed that this indeed how it works in birds. EDIT: After skimming the Wikipedia article, both articles agree that it is a possible but not yet confirmed mechanism.
dnautics 10y ago
The cryptochrome hypothesis doesn't require detachment from the retina as it's a protein that has directional excitatory preference, not the whole cell.
- kakarot 10y ago
  Interesting. Thanks for the clarification. I find this topic to be of extreme interest

fizixer 10y ago

> ... chemistry is a leaky abstraction ... Well I second you on that. Even stronger: All of (theoretical) science is a leaky abstraction. When an area is new, people are doing the spherical-cow-approximation willy nilly. After it gets established, corner cases start to surface. Incidentally, theoretical physicists are the masters of creating spherical-cow-approximations and leaky-abstractions. They're always going for the next big unexplored territory. E.g., once QM got established as a theory, they moved on to high-energy, while there is about 1000x more work to be done picking up the pieces of QM in the areas of solid-state-physics and molecular-chemistry. (largely speaking that is; not everyone is like that).

sriku 10y ago
A meta spherical cow?
jp3141 10y ago
relevant xkcd https://www.xkcd.com/435/ https://www.xkcd.com/435/
- Noseshine 10y ago
  Math is a tool. It's orthogonal and used by all, not hierarchical above (or below) all of them.. http://euclid.trentu.ca/math/sb/misc/mathsci.html http://euclid.trentu.ca/math/sb/misc/mathsci.html > The natural sciences investigate the physical universe but mathematics does not, > so mathematics is not really a natural science. This leaves open the subtler > question of whether mathematics is essentially similar in method to the natural > sciences in spite of the difference in subject matter. I do not think it is. I'm not even including that famous Einstein quote about math. Example: When you are doing math in economics you are not doing something that is even more foundational than physics.
  - rpwverheij 10y ago
    what if the nature of the physical universe has no other reason to be as it is other than mathematical consequences of harmonies, resonances, balances, etc? In other words: if all that exists follows mathematical law, doesnt that make math part of the existential?

sriku 10y ago

Good summary. Classical physics is not good enough for chemistry. So why are we surprised that without a quantum foundation, biology cannot function at all? OTOH, we have a theory that classical computation adequately accounts for intelligence. Finding an unavoidable quantum route that nature has picked would certainly be interesting, despite that quantum Turing machines are also classically computable (I think).

eli_gottlieb 10y ago
>OTOH, we have a theory that classical computation adequately accounts for intelligence. Finding an unavoidable quantum route that nature has picked would certainly be interesting, despite that quantum Turing machines are also classically computable (I think). I don't think we have a foundation for classical computation without thermodynamics, which is a classical theory whose ultimate foundations probably require quantum information theory.

nabla9 10y ago

>in some cases chemistry is a leaky abstraction There has never been "classical" theory for chemistry like there has been classical mechanics that works reasonably well within limits, just weird heuristic rules. Chemistry is quantum chemistry is quantum electrodynamics.

Gatsky 10y ago

Can you provide an example of how this rather facile assertion leads to any insight into biology? For example, how does it follow in a coherent fashion that the chemical properties of DNA lead to Mozart, or a lady bug? In short, how does chemistry explain either the origin, function or future trajectories of any of the utterly amazing biological entities that exist today?

kenbellows 10y ago
I mean... evolution explains the complexity of things, and evolution certainly has a foundation in the chemistry of DNA. Or are you asking why we have the particular configuration of biological entities we have instead of a different one?
- Gatsky 10y ago
  Well what does it mean to say that Biology is applied Chemistry? To me it says 2 things. 1 - That there is no 'new' knowledge in biology. 2 - The important aspects of biology can be reduced easily to applied chemistry. Evolution contradicts this, because it is a genuinely new idea. Some may say it is the ONLY new idea in biology, but that's good enough. It's often quoted here that "Computer Science is no more about computers than astronomy is about telescopes." You could extend this to "Biological science is no more about chemistry..."

anotheryou 10y ago

Or: If it can be optimized/exploited by evolution, of course it will be.