9 ms·

An important quantum algorithm may be a property of nature

163 points by pisky 7y ago

carbocation 7y ago
This is a bit of a tangent (that the author takes): “But during protein assembly, each amino acid must be chosen from a soup of 20 different options. Grover’s algorithm explains these numbers: a three-step quantum search can find an object in a database containing up to 20 kinds of entry. Again, 20 is the optimal number.” 20 is the number of amino acids, but this is ignoring stop codons (and specialized amino acids used for initiation). It’s not super clear to me at what level of abstraction the search is taking place - it can’t be the tRNA space because that’s not just 20 options. The point that electrons seem to follow a Grover search is cool. I’m just unclear on whether the biological part holds up.
- jerf 7y ago
  I'd go farther; I can't even imagine in what way matching a codon to a physical amino acid and attaching it to a protein in progress is a "database lookup" in a Grover database lookup. If proteins were created by the cells by selecting proteins out of quantum superpositions of all the possible amino acids, sure. But that doesn't seem to remotely describe how that process works.
mindviews 7y ago
"The Grover search as a naturally occurring phenomenon" arXiv link: https://arxiv.org/abs/1908.11213 https://arxiv.org/abs/1908.11213
Iv 7y ago
A reason why I allow myself some skepticism on the feasibility of quantum computing is that if it were possible, I would have expected evolution to have used it somehow. If it turns out that protein folding really use a quantum computation, I'll move quantum computers from the "too good to be true" category to the "probably revolutionary stuff that I will see in my lifetime" alongside with nuclear fusion and strong AI.
- teraflop 7y ago
  > if it were possible, I would have expected evolution to have used it somehow. That seems reasonable as long as you're consistent in applying the same skepticism to other inventions, such as the internal combustion engine and the wheel.
  - Iv 7y ago
    The physical principles behind combustion engines and the wheel are displayed in many life forms. Their engineering constraints and goals differ. It is, however, reasonable to expect evolution to find a way to exploit quantum algorithms as it is very useful to several fitness advantages and is something that you would expect to be achievable through protein manipulations.
  - aaron_m04 7y ago
    Bacterial flagella are rotary, so very close to being wheels.
  - SolarNet 7y ago
    Fossil fuels are primarily biological in origin. Certainly we extract the energy in a much different way, but that energy capacity is there biologically (slow burn, turns out high speeds aren't actually that useful in nature). As for wheels, hip joints are a more efficient design of a rotatory system (multiple degrees of freedom). Wheels are much too simple a design to see much use in nature.
- quotemstr 7y ago
  Your argument doesn't stand up to cursory examination. There are all sorts of tricks of physics that evolution never found out how to use. Natural systems don't use the (macroscopic) wheel either, but that works great. Refrigeration works great, but nature doesn't use that either. Complex life has barely been around 540 million years ago. Why would you suppose evolution would have had time to explore the entire space of techniques that physics allows?
  - Iv 7y ago
nicwilson 7y ago
Hmm, there are several things I find strange about this article. There are 22 proteinogenic amino acids (admittedly two are rare, selenocysteine and pyrrolysine, but with rarity comes importance when they do occur). The search for the correct amino acid is not class balanced, e.g. the aromatics are much less common. The tRNAs are also not equally distributed, neither in the codon-anticodon pairing, the aromatics are coded for by only one or two, I suppose this is somewhat reflected in the frequency (see above). Even within one amino acids possible tRNA the ratio's are species dependant to a remarkable degree (see codon optimisation in genetic engineering. You can also tell by sequence analysis if horizontal transfer has occurred if the frequencies are all wrong) and is used to regulate synthesis. e.g. if a species has tRNA UUU : tRNA UUC of 3 : 1 then (classically) one would expect a protein incorporating phenylalanine as UUC to take 3 times longer than UUU to incorporate.
- zahreeley 7y ago
  appreciate the author man. No crib
- knzhou 7y ago
  This is all correct, and shows why both biologists and physicists don't take the conclusions of Patel's paper too seriously. Just aiming for "20" without any context for what that means is a bad kind of numerology. There's probably a grain of truth in the paper, but only enough to get to something like "20 plus or minus 10", not exactly "20". Speaking as an MIT alumnus, some of the school's promotional material is glitzy on the outside and hollow on the inside. The MIT Tech Review's "Emerging Technologies" column is particularly bad. I've written numerous rants over the years rebutting incredibly misleading viral articles from it. It's a shame that people automatically trust it because of the MIT name.
  - jessriedel 7y ago
    MIT Tech Review is no longer associated with MIT. The name is historical vestige. It's just another magazine like Popular Science.
imvetri 7y ago
Everything inside living organisms are learnt from nature. organisms with sight, learn from what it could see. Organisms with sense of sound can create only what it had heard in past. Now imagine primitive organisms that has distributed/scattered sensory system like plants( don't start an argument that plant isn't an organism. instead start the right argument with most flawed system please) We cannot create anything new which we haven't learnt in the past. WE CANNOT CREATE ANYTHING NEW WHICH WE HAVENT LEANRT IN THE PAST. Great people are not great in finding relation in surroundings. They are only good at finding what's inside their brain. What goes inside the brain ? millions of years of nature's influence.
- imvetri 7y ago
  We gotta turn around and rethink how we are educating ourselves and surrounding us. We have to be very careful in not misinforming facts or the way we think.
  - imvetri 7y ago
    Imagine boolean concept in the computer science. The first guy who theorised did he just propose something randomly and error free, or was he able to look / observe how his brain thinks ? I would pick the second one. This is an example that anything that feels flawless is from within ourselves!
jjtheblunt 7y ago
Modal verb ("may") clickbait alert?

163 points by pisky 7y ago

This is a bit of a tangent (that the author takes): “But during protein assembly, each amino acid must be chosen from a soup of 20 different options. Grover’s algorithm explains these numbers: a three-step quantum search can find an object in a database containing up to 20 kinds of entry. Again, 20 is the optimal number.” 20 is the number of amino acids, but this is ignoring stop codons (and specialized amino acids used for initiation). It’s not super clear to me at what level of abstraction the search is taking place - it can’t be the tRNA space because that’s not just 20 options. The point that electrons seem to follow a Grover search is cool. I’m just unclear on whether the biological part holds up.

jerf 7y ago
I'd go farther; I can't even imagine in what way matching a codon to a physical amino acid and attaching it to a protein in progress is a "database lookup" in a Grover database lookup. If proteins were created by the cells by selecting proteins out of quantum superpositions of all the possible amino acids, sure. But that doesn't seem to remotely describe how that process works.

mindviews 7y ago

"The Grover search as a naturally occurring phenomenon" arXiv link: https://arxiv.org/abs/1908.11213 https://arxiv.org/abs/1908.11213

Iv 7y ago

A reason why I allow myself some skepticism on the feasibility of quantum computing is that if it were possible, I would have expected evolution to have used it somehow. If it turns out that protein folding really use a quantum computation, I'll move quantum computers from the "too good to be true" category to the "probably revolutionary stuff that I will see in my lifetime" alongside with nuclear fusion and strong AI.

teraflop 7y ago
> if it were possible, I would have expected evolution to have used it somehow. That seems reasonable as long as you're consistent in applying the same skepticism to other inventions, such as the internal combustion engine and the wheel.
- Iv 7y ago
  The physical principles behind combustion engines and the wheel are displayed in many life forms. Their engineering constraints and goals differ. It is, however, reasonable to expect evolution to find a way to exploit quantum algorithms as it is very useful to several fitness advantages and is something that you would expect to be achievable through protein manipulations.
- aaron_m04 7y ago
  Bacterial flagella are rotary, so very close to being wheels.
- SolarNet 7y ago
  Fossil fuels are primarily biological in origin. Certainly we extract the energy in a much different way, but that energy capacity is there biologically (slow burn, turns out high speeds aren't actually that useful in nature). As for wheels, hip joints are a more efficient design of a rotatory system (multiple degrees of freedom). Wheels are much too simple a design to see much use in nature.
quotemstr 7y ago
Your argument doesn't stand up to cursory examination. There are all sorts of tricks of physics that evolution never found out how to use. Natural systems don't use the (macroscopic) wheel either, but that works great. Refrigeration works great, but nature doesn't use that either. Complex life has barely been around 540 million years ago. Why would you suppose evolution would have had time to explore the entire space of techniques that physics allows?
- Iv 7y ago

nicwilson 7y ago

Hmm, there are several things I find strange about this article. There are 22 proteinogenic amino acids (admittedly two are rare, selenocysteine and pyrrolysine, but with rarity comes importance when they do occur). The search for the correct amino acid is not class balanced, e.g. the aromatics are much less common. The tRNAs are also not equally distributed, neither in the codon-anticodon pairing, the aromatics are coded for by only one or two, I suppose this is somewhat reflected in the frequency (see above). Even within one amino acids possible tRNA the ratio's are species dependant to a remarkable degree (see codon optimisation in genetic engineering. You can also tell by sequence analysis if horizontal transfer has occurred if the frequencies are all wrong) and is used to regulate synthesis. e.g. if a species has tRNA UUU : tRNA UUC of 3 : 1 then (classically) one would expect a protein incorporating phenylalanine as UUC to take 3 times longer than UUU to incorporate.

zahreeley 7y ago
appreciate the author man. No crib
knzhou 7y ago
This is all correct, and shows why both biologists and physicists don't take the conclusions of Patel's paper too seriously. Just aiming for "20" without any context for what that means is a bad kind of numerology. There's probably a grain of truth in the paper, but only enough to get to something like "20 plus or minus 10", not exactly "20". Speaking as an MIT alumnus, some of the school's promotional material is glitzy on the outside and hollow on the inside. The MIT Tech Review's "Emerging Technologies" column is particularly bad. I've written numerous rants over the years rebutting incredibly misleading viral articles from it. It's a shame that people automatically trust it because of the MIT name.
- jessriedel 7y ago
  MIT Tech Review is no longer associated with MIT. The name is historical vestige. It's just another magazine like Popular Science.

imvetri 7y ago

Everything inside living organisms are learnt from nature. organisms with sight, learn from what it could see. Organisms with sense of sound can create only what it had heard in past. Now imagine primitive organisms that has distributed/scattered sensory system like plants( don't start an argument that plant isn't an organism. instead start the right argument with most flawed system please) We cannot create anything new which we haven't learnt in the past. WE CANNOT CREATE ANYTHING NEW WHICH WE HAVENT LEANRT IN THE PAST. Great people are not great in finding relation in surroundings. They are only good at finding what's inside their brain. What goes inside the brain ? millions of years of nature's influence.

imvetri 7y ago
We gotta turn around and rethink how we are educating ourselves and surrounding us. We have to be very careful in not misinforming facts or the way we think.
- imvetri 7y ago
  Imagine boolean concept in the computer science. The first guy who theorised did he just propose something randomly and error free, or was he able to look / observe how his brain thinks ? I would pick the second one. This is an example that anything that feels flawless is from within ourselves!

jjtheblunt 7y ago

Modal verb ("may") clickbait alert?