Re: Kolmorgorov Complexity and Kim Øyhus


Kim G. S. Øyhus wrote:
> In article <1138422549.430709.313780@xxxxxxxxxxxxxxxxxxxxxxxxxxxx>,
> Seanpit <seanpitnospam@xxxxxxxxxxxxxxxxxxxxxxxxxxx> wrote:
> >
> >Kim G. S. Øyhus wrote:
> >
> >< snip >
> >
> >> >The minimum size for a particular function of a protein string of
> >> >residues, as part of a larger system of function, is not the same thing
> >> >as it's minimum size that could be coded for by a Turing machine.
> >> >These are different forms of potential compression. One form requires
> >> >that the function of the protein string be maintained while the other
> >> >does not.
> >>
> >> Again completely wrong. The protein string could be generated from an
> >> organic Turing machine with organic maintenance. But you are not
> >> capable of understanding why this is an argument and what it is an
> >> argument for.
> >
> >Sure a protein string could be generated from by organic Turing machine
> >from a much more compressed state. However, what I'm trying to get
> >across to you is that the compressed state will not work. Only the
> >decompressed state will actually work to do the job as part of a larger
> >system of function.
>
> Yep, you were incapable of understanding my argument.
>
>
>
> >For example, a proteins sequence, like a lactase sequence, could indeed
> >be compressed down to a very few characters. However, these few
> >characters, in their compressed state, would not be able to work as a
> >lactase. Now, they may be able to be decompressed by the proper Turing
> >machine. But, until this happens, they will not have the lactase
> >function.

Actually, the role of enzymes is that of a catalyst. The function of
lactase does not need a catalyst in order to *occur*. It needs a
catalyst only to occur at a rate that is useful to the organism. In
some environments (high heat, acidity) the rate of spontaneous cleavage
of the betagalactosidase bond is higher even in the absence of an
enzyme. [Oh, and all chemical reactions are reversible.]

> You still have not understood that it must work if it is to be a
> proper compression.
>
>
> >So, you see, the lactase function requires a minimum uncompressed size
> >and specificity to work at a beneficial level within the bacterial
> >"system".

IOW, you are talking about *rate* of reaction which is a quantitative
measure and not a qualitative one. So you need to ask "What features
are needed to produce a given level of reaction and do those features
pre-exist in organisms?" You don't ask those questions.
>
> You still have not understood that it must work if it is to be a
> proper compression.
>
>
> >Of course you won't understand the difference here, but the difference
> >is quite significant. The minimum sequence requirements needed to
> >obtain the lactase function to a selectable degree have little to do
> >with the KC of the lactase sequence. They aren't the same.
>
> You still have not understood that it must work if it is to be a
> proper compression.
>
>
> >< snip >
> >
> >> You have misunderstood this completely. The compressed minimal DNA
> >> sequence would somehow construct a biological decompresser. But again,
> >> you will not understand this argument. I even suspect that the
> >> filament of that flagellar moving system is generated by such a
> >> biological decompressor, since it has such a very long repetitive
> >> structure.
> >
> >Sure it is. But, until this minimum is in place, decompressed, the
> >flagellar motility system will not "work" at all. Function of this
> >system requires a certain *decompressed* minimum which has nothing to
> >do with how much the sequence was or could be compressed. Come on now,
> >this is a simple concept.
>
> You still have not understood that it must work if it is to be a
> proper compression.
>
>
> >< snip >
> >
> >> >It's certainly not the minimum functional sequence although it might
> >> >actually be the minimum sequence produced by a particular Turing
> >> >machine.
> >>
> >> Sigh. K.C. usually uses Turing machines as reference computers, but
> >> that is NOT a requirement. The requirement is that the machines are
> >> universal computers, and there are other systems besides Turing
> >> machine that can do that, like Cellular Automatin 110, Combinatory
> >> Logic, Lisp, and biological machinery in the cell, ribosomes & Co.
> >>
> >> The point is, and has been for very long: Cells can be universal
> >> computers.
> >
> >Yes, cells can be universal computers, but this doesn't change the fact
> >that the final functional uncompressed product requires a certain
> >minimum sequence size and specificity regardless of the nature of the
> >underlying code - compressed or not. In other words, the actual
> >functional requirement of the system has nothing to do with its
> >potential for compression - i.e., KC.
>
> You still have not understood that a minimum sequence IS a
> compression, per definition.
>
>
> >< snip >
> >
> >> >> It has lost its output.
> >> >
> >> >It has only lost it's output as far as its original system is
> >> >concerned.
> >>
> >> If it has lost its output, then it is not a compression.
> >
> >Look, a particular protein sequence could be turned into another much
> >more compressed sequence which retains all the information content of
> >the original uncompressed protein sequence. A biological universal
> >computer could restore the compressed sequence to its original
> >uncompressed state. However, the compressed version will not have the
> >biological function of the uncompressed version. It, combined with the
> >proper universal computer, may contain all the needed information to
> >produce the uncompressed version, but until this happens, the function
> >of the uncompressed version will not be realized at all.
>
> You still have not understood that it must work if it is to be a
> proper compression.
>
>
> >For example, DNA stores all the information needed to code for the
> >functional proteins. However, the DNA sequence itself does not perform
> >the function of the protein sequence. The information has to be
> >translated first into a protein sequence, which can then perform the
> >function of a FliG sequence in a flagellar system or a lactase enzyme
> >in an energy metabolic pathway etc.
>
> And the translator mechanisms are also encoded in DNA.
>
> If the translator mechanism is not encoded in DNA, then the DNA is not
> a complete working sequence.
>
> If the decompressor is not encoded into the string, then it is not a
> compressed sequence, and it is not a complete working sequence.
>
>
> >So, you see, it doesn't matter if a sequence could be highly compressed
> >or not. Having low or high KC makes absolutely no difference as far as
> >the minimum size and specificity requirements of a particular protein
> >to do a particular function as part of a particular system.
>
> You still have not understood that it must work if it is to be a
> proper compression.
>
>
> >> >> Your argument is wrong and stupid.
> >> >
> >> >Actually, I believe your argument that functional minimums are the same
> >> >thing as KC is what is off base here.
> >>
> >> You believe a lot of wrong stuff.
> >
> >I suppose that's why we disagree.
>
> Yes.
>
>
> >> >> Your definition of functional complexity did not include that it
> >> >> should be a part of a system of function, so your argument is wrong.
> >> >
> >> >My definition of functional complexity always included the part a
> >> >particular sequence plays in the overall system of function. The
> >> >functional complexity of this part, as part of the whole, is determined
> >> >by the minimum size and sequence specificity requirements that are
> >> >needed in order for it to do its job in a beneficial way relative to
> >> >the system as a whole. In other words, what is the minimum size and
> >> >specificity requirement for a particular sequence to have the lactase
> >> >function to a minimally selectable benefit to the bacterium as a whole
> >> >in a lactose rich environment? Can this minimum be achieve with just 3
> >> >residues? 10 residues? 100 residues?
> >> >
> >> >You see my point?
> >>
> >> I see that you remember wrongly about what you yourself write.
> >> And I can supply you with your definition yet again as evidence that
> >> you are wrong and I am right.
> >
> >It should have been quite clear to you, from the beginning, that my
> >definition of functional complexity was indeed all about systems of
> >function. Nothing functions all by itself. The function of something is
> >always related to something else. Functional parts of a system are
> >interdependent. It is this interdependent nature of a system of
> >function that makes it functionally complex. Every part is dependent
> >upon other parts to produce the united function. That is why a minimum
> >size and specificity part requirement is needed to achieve a particular
> >type of system with a particular type of function. If you misunderstood
> >this I'm sorry.
>
> You are wrong, because living systems do contain independent parts.
>
>
> >> >Chaotic systems are theoretically deterministic (well, not quite), but
> >> >in practice they aren't deterministic - because of those little
> >> >perturbations you mention. "A system may be perfectly deterministic in
> >> >principle, but its behavior is completely unpredictable in practice.
> >> >This phenomenon was called deterministic chaos." The resulting
> >> >"chaotic" outcome of such a theoretically deterministic system ends up
> >> >having the appearance of true randomness. In this sense then nothing
> >> >is actually random. It only has the appearance of randomness because
> >> >of the chaos problem - i.e., the starting parameters are not known and
> >> >cannot be known, even in theory, to an infinite degree. Therefore,
> >> >randomness and chaos are very closely tied together. What appears to be
> >> >"random" only has this appearance because of chaos theory - because the
> >> >starting parameters where not perfectly knowable.
> >> >
> >> >http://pespmc1.vub.ac.be/CHAOS.html
> >>
> >> Thus, chaos has low K.C. while randomness has maximally high K.C.
> >> In other words: Chaos and radomness are maximally different in their
> >> complexity.
> >
> >The notion of randomness is dependent upon chaos.
>
> No.
>
> The notion of randomness is dependent on statistics, entropy, maximal
> K.C., maximal Chaitin complexity.
>
> Chaos is deterministic.
>
>
> >The degree of the
> >unknown factors influencing a system is what makes it chaotic over time
> >- i.e., unpredictable or random.
>
> No. It is nonlinear feedback that makes a system chaotic.
>
>
>
> >That is what a "fair" coin toss is
> >thought to "randomly" land on either heads or tails.
>
> I coin toss is random, not chaotic. You have misunderstood chaos.
>
>
> >This appearance
> >of randomness isn't actually random at all. It is just that the factors
> >influencing the coin toss and/or the roll of the dice cannot be
> >completely known. So, the outcome of either heads or tails or double
> >sixes or double ones seems random. The notions of chaos and randomness
> >are therefore very closely tied together. The outcome of a chaotic
> >system appears to have greater and greater randomness and KC over time.
> > Therefore, as the longer the chaotic system runs, the greater the
> >apparent KC and randomness. But, of course, this is just an appearance
> >that is the result of a lack of absolute knowledge of the starting
> >factors.
>
> No. The K.C. of a chaotic system as a function of time is constant.
>
>
> >> >The minimum size and specificity requirements are a big part of what it
> >> >takes for a piece of a system to be beneficial relative to the whole.
> >> >This has always been strongly implied from the get go Kim. You're just
> >> >trying to build a strawman here.
> >>
> >> You imply that beneficial relative to the whole MUST mean that the
> >> parts are interdependent. Yet again wrong, and with no evidence.
> >
> >The parts of a flagellar system are interdependent. Without FliG, the
> >flagellar motility could not be realized. The same thing goes for FliD
> >and for almost all of the other subsystem parts. I don't see how you
> >can really say, "Yet again wrong, and with no evidence" when my
> >observation here is downright elemetary.
>
> Neutral mutations imply independent parts.
>
>
> >> And since I quoted your writing werbatim, I gave evidence, not a
> >> strawman, but what you actually really wrote.
> >
> >Don't tell me you haven't seen me write extensively about "subsystem"
> >functions and subpart specificity?
>
> I accepted the definition you provided.
> If you use another definition than you provide, then you will be
> misunderstood, and it will be entirely your fault.
>
>
> >Why do you think the specific
> >location of residues is so important to the overall function of the
> >protein as part of an even larger system of function?
>
> I do not think that.
>
>
> >- Because the
> >protein's residues are actually subsystem parts of the larger protein's
> >system of function.
>
> There are neutral mutations.
>
>
> >Such a system requires that its subparts be in
> >their proper number and in their proper places for the system as a
> >whole to actually work.
>
> There are neutral mutations.
>
>
>
> >> >> As for specificity: You have shown that you do not know what
> >> >> specificity is, through your thorough confusion of specificity with
> >> >> density, so I ignore that part of your definition, since you do not
> >> >> know what that part means.
> >> >
> >> >This is ridiculous. Sauer and Olson and even Yockey, as well as many
> >> >others, talk about the minimum sequence specificities of proteins. You
> >> >just can't change too many residues at the same time without a complete
> >> >loss of that protein's function. That's specificity. It can be
> >> >measured. All functional proteins have a minimum specificity
> >> >requirement that can be reasonable determined.
> >>
> >> And thank you for yet more evidence that you do not know what
> >> specificity is. Hershey and other have told you very many times now
> >> what you do wrong, but as usual it goes over your head.
> >
> >Why don't you explain to me what the proper term is for the fact that a
> >fairly specific order of the residues in a protein sequence is required
> >for that protein's function to be realized. You just can't put 400aa
> >together at random and expect to get a lactase. A specific sequential
> >order is required. What name would you give this requirement besides
> >sequence "specificity"?
>
> And thank you for yet more evidence that you do not know what
> specificity is.
>
>
> >> >Irreducible complexity is not totally different from functional
> >> >complexity. IR is all about the minimum size and specificity requirement
> >> >for a particular functional system. That's exactly what I'm talking
> >> >about. All functional systems have a minimum irreducible requirement
> >> >in order for a particular function of that system to be realized. What
> >> >the heck did you think I was talking about this entire time?
> >>
> >> HEY! Now you gave yet another very different definition of Functional
> >> Complexity. This time it is THE SYSTEM that is required to be minimal,
> >> while the definition I quoted from you require that it is the minimum
> >> size required to ACHIEVE a function.
> >>
> >> So, you have given us at least 3 different definitions of functional
> >> complexity:
> >>
> >> 1. A system which is easily destroyed.
> >
> >That's true.
>
> Noted.
>
>
> >> 2. A system which has a description which is as simple as possible.
> >
> >That's not true. A system with high functional complexity requires a
> >large minimum size and *specificity* requirement.
>
> A self contradiction.
>
>
> >> 3. A system which is as small as possible.
> >
> >That's also not true. As noted above, a system with high functional
> >complexity requires a larger minimum size.
>
> Your argument is irrelevant to your conclusion.
>
>
>
> >> >> I seriously thing there is something wrong with your
> >> >> mind, since you are not able to remember stuff people tell you again
> >> >> and again and again ad nauseam. It seems you have lost your ability to
> >> >> learn.
> >> >
> >> >It is just that what you tell me again and again at nauseam is clearly
> >> >wrong as I see it.
> >>
> >> But you do NOT see it, so you are inhabil. You do not see what I mean.
> >
> >And you do not see what I mean. So, we're even ; )
>
> I do see what you mean.
>
>
> >> >The type of simple gas mentioned by Baranger here, if you actually took
> >> >the time to read the paper, is actually an ordinary stationary
> >> >non-turbulent gas in a chamber. The gas molecules still move around
> >> >quite rapidly however. The movements of these molecules are indeed
> >> >non-linear or chaotic (i.e., not predictable over very short periods of
> >> >time).
> >>
> >> Thank you.
> >> Such a gas is not chaotic, while its molecules might be for short times.
> >
> >Baranger IS talking about the location of the actual molecules. Read
> >the paper for goodness sakes! The location of the molecules becomes
> >truly unknowable, i.e., chaotic/random/mixed after just a very short
> >span of time. It is in this way that the gas is actually chaotic. That
> >is why Baranger referred to the gas in the non-turbulent gas chamber as
> >chaotic. It is chaotic in that it's molecules are quickly randomized
> >via the non-linear nature of the problem of predicting where they will
> >be (i.e., chaos).
>
> This is precisely what I wrote about, so I understand the paper
> without reading more of it.
>
>
> >> >> Calling a stationary gas chaotic is not right.
> >> >
> >> >Sure it is. You just don't understand that Baranger is talking about
> >> >the gas molecules - since you obviously haven't read the paper.
> >>
> >> I know perferctly well what it is about, because I know this stuff,
> >> being a real physicist and all, while you just are an arrogant
> >> ignorant making up stuff and believing in it.
> >>
> >> And what I writes show this to be true, but you do not process what I
> >> read, and write a lot of lies about my state of mind.
> >
> >What you have written in this case only shows that you haven't read the
> >paper.
>
> Then there should be disagreement between me and the papir. The only
> disagreement is in your head.
>
>
> >> >> The normal thing to
> >> >> call the molecules of a stationary gas is "random". There is a certain
> >> >> chaotic component to the interaction of the molecules of the gas, but
> >> >> the molecules interacting chaotically does not mean that the gas is
> >> >> chaotic.
> >> >
> >> >What? Molecules interacting chaotically doesn't mean that gas is
> >> >chaotic? How do you arrive at that conclusion? Baranger is talking
> >> >about this chaotic movement of the gas molecules and that is why he
> >> >said, "The simple gas mentioned earlier is highly chaotic, but it is
> >> >not complex in the present sense."
> >>
> >> "The law of large numbers."
> >> The gas is not dependent on the details of its constituent particles.
> >> (Especially not when it just sits there, doing nothing.)
> >
> >We aren't talking about the behavior of the gas as a whole here. We are
> >talking about the individual molecules here. Read the paper Kim.
>
> You only verify my impression of the article.
>
>
> >> Or in other words: 2 gases with the same number of particles,
> >> temperature and container, will behave the same macroscopically,
> >> especially when they just lie there, doing nothing.
> >
> >We aren't talking about the macroscopic behavior of the gas here. We
> >are talking about the location of the molecules here. The location of
> >these molecules is "complex" in the KC sense of the term. However, this
> >has nothing to do with functional complexity. That's the whole point.
> >That is why Baranger says that this sort of complexity is not "complex
> >in the present sense". What do you think he means when he says, "in
> >the present sense"? He is trying to show the difference between
> >functional complexity and Kolmogorov complexity (i.e., randomness or
> >high KC as a result of chaotic interactions over time).
>
> You have misunderstood his article.
>
>
> >> >Chaos is not just the result of a simple formula with a knowable
> >> >outcome. Chaos is more than that. Chaos must contain a component of the
> >> >unknown. The same thing is true of randomness. This is why a string
> >> >that appears random or "chaotic" might actually be the result of a very
> >> >simple formula. In other words, there is no such thing as absolute
> >> >randomness or even chaos. There is only the appearance of randomness
> >> >or chaos because of the involvement of the unknown.
> >>
> >> You are obviously not familiar with Quantum mechanics either. Not a
> >> surprise. I will not even bother to try to explain what that means.
> >
> >I am familiar with Quantum mechanics. What about Quantum mechanics is
> >unknowable given all the information in the universe? Can you prove
> >that quantum mechanics actually involves true randomness?
>
> You lie again. You are not familiar with quantum mechanics at all. I
> can prove that quantum mechanics actually involves true randomness.
>
>
> >> >> >Both apparent chaos and randomness can be
> >> >> >generated by short programs, but the result is unknowable.
> >> >>
> >> >> And now you are again confusing chaos with randomness.
> >> >
> >> >There you go again, thinking that chaos and randomness aren't related.
> >>
> >> One has low complexity, the other high. Very different.
> >
> >The KC and the randomness of a chaotic system both increase over time.
> >Not very different.
>
> The K.C. of a chaotic system do not increase as a function of time.
>
>
> >> >> >That's what
> >> >> >makes chaos and randomness what they are - "unknowable" or
> >> >> >"unpredictable".
> >> >>
> >> >> Chaos is deterministic. You have misunderstood, as usual.
> >> >
> >> >But that's just it. Chaos isn't completely deterministic in practice.
> >> >That's why chaos theory was born, because many things just aren't
> >> >linearly deterministic. To the degree that the unknown is involved and
> >> >can affect outcome, to that degree is chaos and/or unpredictability
> >> >increased over time.
> >>
> >> Yes, but that is not the same as true randomness.
> >
> >There is no true randomness.
>
> Wrong.
> Chaitin proved that there is true randomness in math and logic.
> There is true randomness in quantum mechanics.
>
>
> >There is only the unknown or apparent
> >randomness. Likewise, there is no true chaos. There is only apparent
> >chaos due to a lack of knowledge which is only magnified over time.
> >Perfect/infinite knowledge would do away with both chaos and
> >randomness.
>
> There is true chaos in nature. The weather.
>
>
> >< snip >
> >
> >> >> >It just doesn't make any more sense now
> >> >> >than it did before.
> >> >>
> >> >> You are simply terrible at thinking.
> >> >
> >> >Ditto ; )
> >>
> >> Ha! I am certified Master of Science in Physics from the most
> >> prestigious university in Norway. This would be impossible if I was
> >> terrible at thinking. Furthermore, I have made new advances in
> >> cryptography and have several patens. Again evidence of being good at
> >> thinking. I understand English, Norwegian, German, and Russion. Even
> >> more evidence of being good at thinking.
> >
> >Oh, don't forget your independent discovery of Kolmogorov Complexity! ;
>
> Of course not.
>
> Kim0


.

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