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.
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.
"our coverage is independent of any influence, including our ownership by MIT."
This article mentions a controversy on the topic:
For instance, not factoring in steric factors (e.g. uncertainty principle) or electron tunneling in the transfer of electrons during photosynthesis or cellular respiration would probably throw off your models. Biochemists are well aware of this; you couldn't effectively understand chemistry without understanding quantum mechanics.
This is actually my main point. I'm not intending to reduce or dismiss (bio)chem through the lens of applied physics. I'm saying that anyone competent in biochem understands these properties on an intuitive level, and further understands that the root of these systems' behavior lies in quantum mechanics, even if they're not crunching wave equations on a daily basis. (That said, discussing s and p orbitals are a pretty routine part of figuring out organic reaction mechanisms.)
The field considers the quantum effects on these systems as a matter of course - as with your example about ion channel flow and caveats on bulk properties versus a single ion. There's still no question that quantum mechanics affects these systems, it's just a question of when it needs to be factored in to not throw off the calculations, and when the scale is large enough that its effects can be considered negligible.
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.
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.
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.
I know that it's fashionable to simply declare quantum computing is impossible, and there are some strong arguments in this direction, but this particular argument isn't one.
The general reason people believe quantum computing is possible is that it describes just about all the things I mentioned above absolutely perfectly, along with literally thousands of other phenomena, with no deviations ever measured. This gives us good reason to assume quantum mechanics actually works, and if it does, then it's possible for quantum computing to work. (Also, of course you need to account for quantum mechanics to account for protein folding. You literally can't have chemical bonds at all without quantum mechanics.)
1. Life may not have a use for it
2. It may be impossible to achieve with proteins and cells
3. It may not actually be possible
For quantum computer I (weakly) believe that 1 and 2 are wrong: evolution and cognition would hugely benefit from quantum acceleration and biology operates at a scale where quantum effects are visible. I thought 3. slightly more likely but I'll readily admit that I am nowhere near the knowledge to be categorical about 2.
And note that of the list of things you are giving, there are many that uses the same physical principles that are used by life: steam engine (expansion of heated gases), rockets (ignition of gas), jets (propulsion), helicopters (a rotating wing is a wing), radio waves/X-rays (the RF spectrum, which visible light is part of), etc... The rest, IMO, falls either under 1. or 2. For instance I doubt long-distance communication really offers a substantive advantage when you know whales can already contact each other at 100s of kilometers through shouts, and superfluidity may require conditions and materials that are impossible to reach for organic material.
Note however that this last one is actually a kinda good (if weak) argument: if superfluidity was achievable through organic material and conditions close to the temperature and pressure average on earth, life would probably have found it, as it is clearly a useful property. If tomorrow we find that you can get room-temperature superfluids that are made out of C,H and O atoms, wondering why it is not found in nature will be a very good question.
There is some extrapolative argument that hints at the contrary. Adrian Thompson's evolved FPGA circuits exploited a single chip's underlying physics in a manner no digital circuit designer would. By that thread, it would seem possible that evolution has already exploited quantum computation ... just that maybe we haven't had the tech eye to see it yet.
After all, all systems are quantum mechanical.
It may turn out to be a similar issue to jet engines, or semiconductors. The materials and conditions required for them to operate just aren't very easy for terrestrial life to evolve into.
Suppose this all started with a few self-replicating proteins. From that we got organelles, and then cells. Then multi-cellular organisms, then tissues, organs, etc.
But working backwards, from protein -> molecular chemistry -> quantum phenomenon, may simply not be the path of least resistance and thus for the overwhelming majority of life in the universe, was not an evolutionary path.
The same thing applies to quantum computers. They’re much much harder to build because they’re more delicate. We’re talking about effects that usually are completely destroyed by a single unwanted atom coming in and hitting something. And there are a lot of atoms flying around in cells. Propagating any quantum signal from even one cell to an adjacent one is impossible. Finally they’re less useful. I can’t think of problems a biological brain needs to solve that require even a moderately fast CPU, let alone a quantum computer, which provides speedups over the CPU for only certain specific problems.
But none of this really matters, because your comment is one long isolated demand for rigor. You wave away my long list of examples because you think something very distantly related exists (in which case, with those low standards, quantum computers already exist), or because the examples are clearly impossible or not useful (without equally seriously considering the same for quantum computers). This is what I mean by skepticism of QC being driven mostly by intellectual fashion.
There are a lot of seeds that are aerodynamic so that they get spread more widely for example. Even seeds that have controlled falls due to "autorotation"
But of course on planet earth at least it is hard for nature to use things requiring too high or low temperatures. Nature doesn't need the Haber process, but it does fixate nitrogen.
So, no, superconductivity probably does not exist in nature
For pretty much every thing you list, nature has something pretty close to it in it. Even nuclear fission.
It's unlikely that enzymes could catalyse fission reactions. It would be amazing if they could...
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.
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.
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.
I suspect we’re just really bad at identifying quantum processes in living things.
The physical principles behind refrigeration are witnessed in several places in nature.
Being able to communicate non-visibly without giving away our position audibly would be a huge advantage (until your predators/competitors figured it out).
Life isn't generally suitable to the use of really high energies like X-rays because it damages cells. It isn't suitable for low energies because it is difficult to create an individual receiving/broadcasting element at such a small scale.
There absolutely are physical phenomena that life does not take advantage of.
x-rays aren't a unique physical phenomena, just a wave length of electromagnetic waves, which is a physical phenomena that life makes excessive use of (photosynthesis, vision).
But yes, the idea is that if there were a physical principle that would be super useful to animals yet not witnessed in nature, that is something that needs to be explained. There are reasons for evolution to miss a solution.
In the case of quantum computing, I could not really see it: the effects happen at a scale where evolution operates, and could easily be integrated, e.g. in nerve cells to create a workable signal. I thought reasonable to make it an element to feed my skepticism, though not a ultimately strong argument to deny any possibility of quantum computing.
So far as I know there's no general theory of theories which quantifies this, so there's no way to make predictions about the cut-off point for evolutionary invention.
But in a hand-wavy way, evolution's only feedback loop is first-order and binary - mutate and reproduce at a positive replacement rate, or not.
The feedback loop in science is more complex. Instead of being driven by a random search, "mutations" are guided by a creative model. This creates momentum in the model space which isn't available to evolution - which in turn makes it possible to discover more complex and less immediately accessible solutions.
It also makes it possible to build systems whose value is guaranteed, or at least strongly suspected, before resources are diverted to making them physical.
The bottom line is evolution is only ever going to find a small subset of all possible biological configurations, and that space is going to exclude many features that are available to science-driven search.
(Of course you can argue that scientific meta-search was a product of evolution anyway, so the distinction is academic.)
I could point to MRIs and SQUID, but I guess you could claim some animals sense magnetism (for wayfinding or determining north). I don't consider those to be in the same league but then we're back to arguing semantics under your definitions.
The fact remains that physical phenomena exist that evolution did not discover. There are perfectly good reasons for that, but I don't think it is fair to say if nature doesn't use it then it is "questionable".
Of course: you need an extremely cold and clean environment, which is very hard to generate in a cell. And it wouldn't even be that useful for cells anyway.
The exact same reasoning applies to quantum computers.
But life could do similar things with collimating reflectors, even for sound. Are there organisms that use geometry to shape sound to send a signal? I'm only aware of ones that use geometry to boost/tune their reception (e.g. owls).
Edit: Dolphins apparently
Wouldn’t this include pretty much any animal than can vocalise?
Arguing that while nature doesn't might not use some technology, it does do something else that relies on the same principle. Who's to draw the line between a technology and a principle? You can say nature has done anything so long as your definitions are uselessly vague.
I continue to believe that it's very likely that brains somehow leverage quantum computing.
The human brain is able to accomplish computational tasks on only around 40 watts of power that destroy what we can accomplish using pretty much any known machine learning algorithm using tens or even hundreds of thousands of watts of power. Maybe our algorithms are primitive or wrong, or maybe the brain just is not a classical computer.
The power of brains is so "unreasonable" that I've long suspected that there are only three possibilities:
(1) Brains are quantum computers.
(2) P=NP, or for a weaker form perhaps there exist large numbers of undiscovered algorithms that offer massive speed improvements over any currently known algorithm.
(3) Brains or intelligence are "supernatural" or at least tap into something about nature that we fundamentally do not understand.
I think option #1 is by far the most likely, especially given that brains excel most of all at search and quantum computing seems to really be able to speed up search.
There is just no way classical computation can do what the human brain does on 40 watts. To me that strains credulity much more than any of the three options above. It just cannot possibly be so.
In a way, your argument makes the same mistakes that it claims these scientists are making.
> strong AI
I'm not sure what you're arguing here; evolution has achieved this in the form of the human mind. I strongly doubt we are as close as some believe to creating SAI, certainly not in the lifetime of any living human being, but arguments that hinge on natural demonstrations require that this is eventually possible.
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.
This is an example that anything that feels flawless is from within ourselves!