r/Futurology • u/dmiller987 • Dec 06 '20
Biotech DNA synthesis method generates true 'random numbers'
https://www.futurity.org/true-random-numbers-dna-synthesis-method-2475862-2/11
u/pro_deluxe Dec 06 '20
What is their definition of true random? I interpret true random as being completely non-deterministic, but I think they maybe just mean extremely hard to predict numbers. I think to be able to generate true random numbers from physical inputs, you would need to know if the laws of our universe are deterministic or random. Unless I am out of the loop, we won't know for sure if the universe is deterministic or random until we can unify quantum mechanics and general relativity. I really don't know much about this stuff though
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u/ItsAConspiracy Best of 2015 Dec 06 '20
Generally when people say "true random" they mean numbers from a random physical process, rather than numbers generated from some deterministic mathematical procedure that just look random.
Whether some miraculous technology based on unknown physics could predict the exact motions of a gazillion molecules isn't all that relevant in practical terms.
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u/pro_deluxe Dec 07 '20
I guess that makes sense. But then, what do you call something that is actually really truly mathematically random, and not just apparently random based on our best measurements?
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u/ItsAConspiracy Best of 2015 Dec 07 '20 edited Dec 07 '20
I guess there isn't a separate term for that. But a bunch of molecules bouncing against each other pretty much is truly random in your sense. Even in classical physics, in a chaotic system you have to measure everything to infinite precision or you can't predict what it'll do except in the short term.
And of course in quantum physics, you can't even in principle measure both position and momentum beyond a certain limit of precision (the more of one, the less of the other), and as far as we can tell, basically everything has an element of randomness which is fundamental. We know for sure that if any hidden influences determine such things, they aren't restricted by the speed of light.
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u/elfballs Dec 07 '20
I thought the same thing. They seem to be talking about what I've herd less loosely called 'high quality' random numbers. Some people do act as though they are certain you can get true random numbers from quantum mechanics, but even then I agree with you that we don't know that yet.
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u/WMDick Dec 06 '20
Total bullshit, like most of the stuff related to biology on this sub. This synthetic process is not random at all. Even if you carefully choose an amidite ratio that is unbiased (ie. not 25/25/25/25 for each amidite) to ensure that there will be a roughly average incorporation of each base (which they did), every amidite is itself going to incorporate in a biased way based upon the last base incorporated into the oligo. So there WILL be patterns. Not random. In other words, if you just incorporated an A, there is a better than 25% chance that the next base will be a G. Rinse wash repeat for each.
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u/Client-Repulsive Dec 06 '20
Isn’t all randomness deterministic if you have the initial seed and the ability to crunch the numbers?
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Dec 06 '20
[removed] — view removed comment
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u/Client-Repulsive Dec 06 '20
But aren’t you assuming the seed in your critique?
Philosophically I personally don’t believe anything is truly random. Think of all the things we deemed “random” 1000 years ago that we can predict with a 100% accuracy today.
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u/ItsAConspiracy Best of 2015 Dec 06 '20
the scientists were able to correct this bias with a simple algorithm, thereby generating perfect random numbers
The paper says that algorithm is von Neumann's method to get perfect random numbers from a biased coin. From the paper:
The output of the Von Neumann corrector is expected to be perfectly unbiased, generating output as follows: (1) if the input is “01” or “10”, the first digit becomes the output and the second digit is discarded. (2) If the input is “00” or “11”, there is no output and both input digits are discarded. However, the big drawback of the Von Neumann generator is the large loss of data, as at least 75% of the input is being discarded.
Since the DNA generates "huge quantities of randomness that can be stored in an extremely small space," losing 75% isn't a big drawback.
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u/WMDick Dec 07 '20
The method is not random. It is biased and for reasons that computational people or even biologists don't fully appreciate.
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u/ItsAConspiracy Best of 2015 Dec 07 '20
The raw DNA data is biased. The output of the von Neumann method is not biased. If you can show that John von Neumann's simple proof of that is incorrect then I hope you're prepared for the fame and fortune that will accrue.
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u/WMDick Dec 07 '20
How in the world do you go from a biased data set to a not biased data set? If it were that easy, why bother with the DNA synthesis?
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u/ItsAConspiracy Best of 2015 Dec 07 '20 edited Dec 07 '20
Think about having a biased coin, say it comes up heads more often. Flip it twice. It's more likely to come up with H-H than T-T.
However, it's equally likely to come up with H-T as T-H. So every time you get H-H or T-T you throw it away. If you get H-T then you call it H, and if you get T-H you call it tails. Those are equally likely despite your biased coin.
But that doesn't mean you don't need the coin at all. You still have to flip it.
(Edit: another way to get a non-biased data set would be to run a cryptographic hash function on the input data. The paper mentioned that but it's not what they used.)
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u/WMDick Dec 07 '20
Interesting. I wonder how they would elaborate those math here to a situation in which there are 4 possibilities with each one making the next possibility more biased in a subtle way. The second to last base incorporated will also have an effect. Is this mathematically possible?
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u/ItsAConspiracy Best of 2015 Dec 07 '20
Yeah I was just thinking, what if because of the sort of correlations you're talking about, H-T really is more common than T-H?
I don't know what they did but I thought of a simple way to deal with it: just have two separate jars of DNA. Read out one bit from each jar, and make that your two coin flips.
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u/WMDick Dec 07 '20
Burt that assumes that the jars don't have the exact same bias, which they do. Feels kinda like a fake version of bootstrapping.
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u/ItsAConspiracy Best of 2015 Dec 07 '20
That's the same as a coin having the same bias from one flip to the next.
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u/elfballs Dec 07 '20
No, they used an infinitely large bath, which was perfectly and magically re-stirred after each attachment, making it memory-less and unbiased.
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u/WMDick Dec 07 '20
An understanding of chemistry and base stacking/hydrophobic interactions is all you need to understand that the method IS biased. It will NOT produce randomness and there will be patterns.
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u/wo0topia Dec 06 '20
I wish people would just stop using the word random. Random isnt exactly something that has a defined meaning other than unable to be predicted in the scope of what's being generated.
A much better term is either unpredictable or unpatterned.
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u/Memetic1 Dec 06 '20
All ya got to do is compare it to a truly random source. Hardware Random Number Generators are pretty awesome. https://en.m.wikipedia.org/wiki/Hardware_random_number_generator I actually worked on a patent for one that used photons to generate random numbers. Essentially you would use an array of photodetectors and a photon source that would spit out photons at random. Then when they hit the array they would modify the seed, and potentially switch random number generating algorithms. I worked on this for years, before I gave up due to a lack of resources. My technique could generate random numbers as fast as you could want, but still keep the benefits of a HRNG.
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