RNAcomputing CAs feasibility

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 Joined: October 13th, 2017, 2:14 am
RNAcomputing CAs feasibility
Are any such things feasible?
And are messengerRNAs imitations by CAs possible? Was the RNAcomputing by L. F. Landweber et al a messengerRNAsimitation?
(Cukras, A.R., Faulhammer, D., Lipton, R.J. and Landweber, L.F.: Chess games: a model for RNA based computation, "BioSystems," Vol.52, pp.3545, 1999.)
And are messengerRNAs imitations by CAs possible? Was the RNAcomputing by L. F. Landweber et al a messengerRNAsimitation?
(Cukras, A.R., Faulhammer, D., Lipton, R.J. and Landweber, L.F.: Chess games: a model for RNA based computation, "BioSystems," Vol.52, pp.3545, 1999.)
Re: RNAcomputing CAs feasibility
I haven't read the paper, but it seems unlikely to be an "imitation" given that it used actual RNA. This question seems just about as vague as your previous question of a few days ago  did you really need another new thread for this one?Koiti Kimura wrote:Was the RNAcomputing by L. F. Landweber et al a messengerRNAsimitation?
From an article in thescientist.com:Abstract of Landweber paper: Here we develop the theory of RNA computing and a method for solving the 'knight problem' as an instance of a satisfiability (SAT) problem. Using only biological molecules and enzymes as tools, we developed an algorithm for solving the knight problem (3 x 3 chess board) using a 10bit combinatorial pool and sequential RNase H digestions. The results of preliminary experiments presented here reveal that the protocol recovers far more correct solutions than expected at random, but the persistence of errors still presents the greatest challenge.
DNA/RNAbased computing does potentially have some commonality with CAs. It's possible to operate on a large area or a large number of potential solutions all at once.Her RNA computer was hailed at the time as the world champion by computer scientist Leonard Adleman of the University of Southern California. But Landweber subsequently chose to move on to other projects. "DNA computing is a difficult field to work in," she explains. "Silicon computers have had a 50year head start, so the bar is set so high for a computation to be a meaningful one that it makes the field of wet computers pretty daunting. We didn't see the killer application, and most people in that field have shifted their interest toward building DNA molecules rather than using DNA molecules to solve problems faster than a computer can."
It seems as if it should be possible to design a CA that starts with a random field and stabilizes into a valid solution to "the knight's problem".  There are at least three different optimization puzzles that have been called "the knight's problem", by the way, but in this case the problem seems to be to put the largest number of knights on an MxN chessboard such that no knight threatens any other knight.
It's hard to see how either RNA or CAs can really make an exciting contribution to this problem, because of the difficulty of designing a system that's guaranteed to come out with an optimal solution instead of just a valid one. In either case you could make a column of candidate solutions in descending order of population, and test them with a CA rule or a physical RNAbased system. The first candidate that doesn't change is an optimal solution.
But that requires preconstructing all candidates. That's easy enough for 3x3, but the task gets exponentially harder as the size increases. So this is certainly not a practical way of finding that optimal solution.

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Re: RNAcomputing CAs feasibility
So, is DNA/RNAbased computing just/merely a kind of probabilistic (guesswork or approximation) computation? But don't the actual DNA and RNAs work on a proper/right nonguesswork/approximation basis/principle for the one valid solution instead of some optimal solution(s)? I mean, aren''t any CAsimitations of such a proper principle feasible?
By the way, believe it or not, I have these P=NP proofs using dmd (diagonal method disproofs) etc. and this 3coloring problem solution utilizing 4Coloring Theorem. If they should be valid/true, would the answer to the last question in my previous paragraph be "yes"?
By the way, believe it or not, I have these P=NP proofs using dmd (diagonal method disproofs) etc. and this 3coloring problem solution utilizing 4Coloring Theorem. If they should be valid/true, would the answer to the last question in my previous paragraph be "yes"?
Re: RNAcomputing CAs feasibility
That's a bit of an outlandish claim, as the P vs. NP problem is one of the most famous and longstanding unsolved problem in mathematics, and the fourcolour theorem required a large amount of computing power to prove. So, I think you're not expressing yourself/explaining correctly what you mean.Koiti Kimura wrote:By the way, believe it or not, I have these P=NP proofs using dmd (diagonal method disproofs) etc. and this 3coloring problem solution utilizing 4Coloring Theorem. If they should be valid/true, would the answer to the last question in my previous paragraph be "yes"?

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Re: RNAcomputing CAs feasibility
I understand very well as commonsensical your opinion about my claim.
But believe me: e. g. , dmd's are so simple/foolproof:
A. 2 < Aleph0, so Aleph1 = 2^Aleph0 ≦ (is equal to or smaller than) Aleph0^Aleph0 = Aleph0 (all by the proofs by Cantor himself);
B. iff Goedel logical formula is G, then G = notprovable (G), then not G = provable (G) = G, and it is contradictory, so the diagonal lemma in Goedel's "Proof" must be wrong.
As you know, all the existent P ≠ (not equal) NP "proofs" use dm's: Fortnow's, Sipser's, etc.
And I also have nonreductioadabsurdum/counterproof, positive/offensive/aggressive/active/nonpassive P = NP proofs.
As for 3coloring, you simply have to trust me, judging from the above dmd's. I fail to know how to upload the graph for the proof.
But believe me: e. g. , dmd's are so simple/foolproof:
A. 2 < Aleph0, so Aleph1 = 2^Aleph0 ≦ (is equal to or smaller than) Aleph0^Aleph0 = Aleph0 (all by the proofs by Cantor himself);
B. iff Goedel logical formula is G, then G = notprovable (G), then not G = provable (G) = G, and it is contradictory, so the diagonal lemma in Goedel's "Proof" must be wrong.
As you know, all the existent P ≠ (not equal) NP "proofs" use dm's: Fortnow's, Sipser's, etc.
And I also have nonreductioadabsurdum/counterproof, positive/offensive/aggressive/active/nonpassive P = NP proofs.
As for 3coloring, you simply have to trust me, judging from the above dmd's. I fail to know how to upload the graph for the proof.
Last edited by Koiti Kimura on May 4th, 2018, 9:35 pm, edited 1 time in total.
 Majestas32
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Re: RNAcomputing CAs feasibility
Koiti Kimura wrote:
As for 3coloring, you simply have to trust me, judging from the above dmd's. I fail to know how to upload the graph for the proof.
Sounds like fermat
Please, stop spam searching Snowflakes.
Re: RNAcomputing CAs feasibility
I have a proof that 1=2, but these forums don't let you make a post big enough to contain it. I have also proven that 2 does not equal 1, and therefore equality is not commutative. You'll just have to take my word for it, trust me, I'm a genius.
succ
 gameoflifemaniac
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Re: RNAcomputing CAs feasibility
But please try to post attachments with the proofs!blah wrote:I have a proof that 1=2, but these forums don't let you make a post big enough to contain it. I have also proven that 2 does not equal 1, and therefore equality is not commutative. You'll just have to take my word for it, trust me, I'm a genius.
I was so socially awkward in the past and it will haunt me for the rest of my life.
Code: Select all
x = 21, y = 5, rule = B3/S23
b2o2bo2b2o2b2o2bobobo$o3bobobobobobobobobo$bo2bobob2o2b2o3bo2bo$2bobob
obobobobo2bo$2o3bo2bobobobo2bo2bo!
 toroidalet
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Re: RNAcomputing CAs feasibility
the problem here, of course, is that the proof requires advanced theorems in the disparate fields of quantum sociology and a conjecture based on Graham's number, and that's just the simplest theorems required. This proof is in an area of mathemology so advanced that no one else has dared to enter it. The proof can't even be uploaded to dropbox or google drive or something; it has trillions of cases identified in its transinfinite induction, not to mention hundredsofpageslong proofs for each involving multiple horrendous quadruple sums. You would probably find the proof completely intractable if you were to read it, so don't even bother, as you likely will get a headache and probably need sleep, as you can't just read it in a year.gameoflifemaniac wrote:But please try to post attachments with the proofs!blah wrote:I have a proof that 1=2, but these forums don't let you make a post big enough to contain it. I have also proven that 2 does not equal 1, and therefore equality is not commutative. You'll just have to take my word for it, trust me, I'm a genius.
And that's just the abstract.
Interestingly, it does prove that Fermat's Last Theorem is false.
(it was supposed to be a joke, blah hasn't actually proven that 1=2. Don't believe everything you hear on the internet, kids.)
"Build a man a fire and he'll be warm for a day. Set a man on fire and he'll be warm for the rest of his life."
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 gameoflifemaniac
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Re: RNAcomputing CAs feasibility
I'm dumbtoroidalet wrote:the problem here, of course, is that the proof requires advanced theorems in the disparate fields of quantum sociology and a conjecture based on Graham's number, and that's just the simplest theorems required. This proof is in an area of mathemology so advanced that no one else has dared to enter it. The proof can't even be uploaded to dropbox or google drive or something; it has trillions of cases identified in its transinfinite induction, not to mention hundredsofpageslong proofs for each involving multiple horrendous quadruple sums. You would probably find the proof completely intractable if you were to read it, so don't even bother, as you likely will get a headache and probably need sleep, as you can't just read it in a year.gameoflifemaniac wrote:But please try to post attachments with the proofs!blah wrote:I have a proof that 1=2, but these forums don't let you make a post big enough to contain it. I have also proven that 2 does not equal 1, and therefore equality is not commutative. You'll just have to take my word for it, trust me, I'm a genius.
And that's just the abstract.
Interestingly, it does prove that Fermat's Last Theorem is false.
(it was supposed to be a joke, blah hasn't actually proven that 1=2. Don't believe everything you hear on the internet, kids.)
I was so socially awkward in the past and it will haunt me for the rest of my life.
Code: Select all
x = 21, y = 5, rule = B3/S23
b2o2bo2b2o2b2o2bobobo$o3bobobobobobobobobo$bo2bobob2o2b2o3bo2bo$2bobob
obobobobo2bo$2o3bo2bobobobo2bo2bo!

 Posts: 24
 Joined: October 13th, 2017, 2:14 am
Re: RNAcomputing CAs feasibility
1. Sorry: my 3Coloring Theorem "proof" has proved to be wrong/false after more careful considerations.
2. But I'm sure you see that my Cantor/GoedelDMd's (Doctorate of Math disqualifications) are absolutely foolproof truths; so, the P=NP proofs that are based on the DMd's or not based on them still live.
2. But I'm sure you see that my Cantor/GoedelDMd's (Doctorate of Math disqualifications) are absolutely foolproof truths; so, the P=NP proofs that are based on the DMd's or not based on them still live.
Re: RNAcomputing CAs feasibility
Okay, now I'm convinced you're just trolling us.Koiti Kimura wrote:(Doctorate of Math disqualifications)

 Posts: 24
 Joined: October 13th, 2017, 2:14 am
Re: RNAcomputing CAs feasibility
NO! I am seriously "eager" (so to speak) for the progress of the math including future CA theories and DNA/RNA computing theories, believe me. If you feel disgusted at my sounding arrogant or provocative, excuse me. But I am a believer in Good Samaritanism, honest! I was wondering if I might be of any help to this field/discipline of math, namely, if I could give the slightest hint for any progress in it, even with the scarcest knowledge of mine. At least, trust in my lack of any malice.
Re: RNAcomputing CAs feasibility
As far as proving Pvs.NP, there are some good (and entertaining) resources out there describing experts in the field who have gotten buried by floods of purported proofs and disproofs by nonexperts, and who eventually have to throw in the towel and declare that they're simply not going to look at any more of them  at least unless they're interestingly different from all the others!Koiti Kimura wrote:I was wondering if I might be of any help to this field/discipline of math, namely, if I could give the slightest hint for any progress in it, even with the scarcest knowledge of mine.
Here's a good list of attempted contributions to the field that got as far as a completed paper (though not a peerreviewed paper, with one single exception out of more than a hundred).
That link also notes that there's a milliondollar Clay Mathematics Institute prize attached to the Pvs.NP question. So 1) if you have a solution, this thread isn't the place for it, and 2) don't expect it to be easy to get past the wall of understandable doubt on the part of any reasonable person reading claims of this kind.
I think this is the statement from an "exhausted Pvs.NP expert" that I remember from years ago:
Back to the intended topic of the thread:Oded Goldreich wrote:In my FAQ page, I stated that I will refuse to check claims regarding the resolution of famous open problems such as P versus NP. I would also advi[s]e other experts to do the same, unless the claim is augmented by a clear and convincing indication as to how this work succeeds where many others have failed.
Needless to say, the famous open problems of Computer Science are very appealing, interesting, and natural. As such, they also attract the attention of nonexperts, and one annoying consequence is a flood of false claims of resolutions of these problems. These claims are never supported by any new insight nor a clear and convincing argument as to what makes the authors believe that they have succeeded where many others have failed. Having the relatively few expert proofread all these false claims would constitute a vast waste of scarce resources.
It is indeed possible that a nonexpert may succeed where experts have failed, but such an event is very unlikely. Furthermore, I believe that in such a case, the successful nonexpert will be able to convince the scientific community that his/her claim is indeed valid, and in particular will be able to bypass or break the ``wall of refusal'' erected in the previous paragraph. In particular, it is most likely, that he/she will be able to present a novel insight that would be intriguing enough to convince experts to read the work.
I do not advocate not thinking about the famous open problems, although in my opinion a fruitful approach would be to try to gain more understanding (via easier related problems) rather than trying to make a superultragiant step.
This still seems too vague to be answerable. If you try to build a CA that's somehow equivalent to the RNA method of solving the "knight's problem", for example, you'll very likely find that that it's not in the least reasonable to model RNA matching with the required "10bit combinatorial pool" inside a CA  it would need too many states, or too much complex structure, ultimately for no useful purpose.Koiti Kimura wrote:So, is DNA/RNAbased computing just/merely a kind of probabilistic (guesswork or approximation) computation? But don't the actual DNA and RNAs work on a proper/right nonguesswork/approximation basis/principle for the one valid solution instead of some optimal solution(s)? I mean, aren''t any CAsimitations of such a proper principle feasible?
What you would really do is throw away the whole RNAcomputing idea and solve the knight problem in some reasonable CAbased way  maybe somewhat analogous to what calcyman did in early versions of apgsearch with special rule tables for removing blinkers and blocks. For example, you might end up with a custom rule that is stable in the presence of a valid solution to the knight problem but unstable otherwise.
Unfortunately that doesn't guarantee a provably optimal solution, so you'd probably have to do a lot more work on the specifics to come up with anything really new or interesting.
Re: RNAcomputing CAs feasibility
Also, if you have a proof of P != NP, then publish it. But if you prove P=NP and create an efficient algorithm for solving NP problems then you have a bit more of a problem.
If you publish the algorithm then everyone's cryptography suddenly stops working at once and you destroy the entire financial system. So you should give some warning before you release the algorithm. But if you let people know who you are then the CIA (or similar) will kidnap you and torture you until you give them the algorithm. So the correct thing to do is to announce your solution anonymously. You can prove that your algorithm works by publishing the solution some preexisting wellpublicised hard NPcomplete problem. Then once people have had some time to understand what's going on you can release the algorithm.
If you publish the algorithm then everyone's cryptography suddenly stops working at once and you destroy the entire financial system. So you should give some warning before you release the algorithm. But if you let people know who you are then the CIA (or similar) will kidnap you and torture you until you give them the algorithm. So the correct thing to do is to announce your solution anonymously. You can prove that your algorithm works by publishing the solution some preexisting wellpublicised hard NPcomplete problem. Then once people have had some time to understand what's going on you can release the algorithm.

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Re: RNAcomputing CAs feasibility
1. I fail to have got any actual concrete NP problems solution algorithms yet. What I HAVE managed to do is prove that they can be solved within the P problems solution time periods in principles, or (in other words), basically somehow (with some unknown methods), and the proofs employed the dmd's or other tools.
2. I would like to give my heartfelt apology to dm supporters because I as a Christian must never look down on them; I take back the jeering remark containing the "Doctorate of Math disqualifications"; I did not mean it; I jotted it down, carried away by Satan's temptation. If it hurt anyone's feelings, excuse me; actually, I willingly admit that Cantor, Goedel and other dm misusers were/are real geniuses and have left great legacies behind: e.g., Cantor, his transfinite arithmetic; Goedel, his Completeness Theorem, which had to be supplemented with Incompleteness/Inconsistency "Theorem" disproofs: those feats of theirs were indispensible for the "GodastheonlyInfinity (InfiniteResourcesPossessor)andunique/singleOmniscient" Christiantheology revealed to me.
2. I would like to give my heartfelt apology to dm supporters because I as a Christian must never look down on them; I take back the jeering remark containing the "Doctorate of Math disqualifications"; I did not mean it; I jotted it down, carried away by Satan's temptation. If it hurt anyone's feelings, excuse me; actually, I willingly admit that Cantor, Goedel and other dm misusers were/are real geniuses and have left great legacies behind: e.g., Cantor, his transfinite arithmetic; Goedel, his Completeness Theorem, which had to be supplemented with Incompleteness/Inconsistency "Theorem" disproofs: those feats of theirs were indispensible for the "GodastheonlyInfinity (InfiniteResourcesPossessor)andunique/singleOmniscient" Christiantheology revealed to me.