Physical question

[Skepdick]

This is a fallacy of "equivocation". Information in DNA is not a program, or a changeable something. If a DNA is set, it keeps replicating itself exactly. It will produce over and over again the same functional proteins.

Have you heard of a quine

A quine is a computer program which takes no input and produces a copy of its own source code as its only output. The standard terms for these programs in the computability theory and computer science literature are "self-replicating programs", "self-reproducing programs", and "self-copying programs".

[-1-]

Chemical work can be reduced to physical work. It is not societal-type work at all. The information you spake of is not information; the expression used is a metaphor.

This is a fallacy of "equivocation". Information in DNA is not a program, or a changeable something. If a DNA is set, it keeps replicating itself exactly. It will produce over and over again the same functional proteins. We use the word "information" because the chemical commands contained within are different from individual to individual. But once it's set, it can't be changed.

So it is not information in the sense that societal work uses information.

It is, instead, a misnomer to call the unchangeable commands in DNA a set of information. Information is a communicated value; nobody communicates via DNA.

OK, if you are so convinced about it, but I believe biochemists/geneticists/molecular biologists would not agree with you, with respect to the claim that this is misnomer or metaphor to call it information, or bioinformaticians, for that matter. And certainly is not unchangeable, otherwise it would not be a subject to mutation and damage repair. And without changes, evolution would be impossible.

Please read more carefully.

Mutation does not occur after DNA is set. I am not a biochemist; but I know that if a mutation occurs then special cells or proteins hunt that mutation down and kill it. People or animals or plants don't change their DNA after it's set. Whatever the proper expression is for "set"-ting. If it changed after a certain point in the individual's development, and kept changing 'till death, then DNA identification would be impossible. But it is not impossible. So DNA does not change after a certain age has been reached by the embrio or by the individual.


It is a semantic point. "Information" is not "information". It seems I am unable to describe for you the difference. For you if one thing is called information, then it's the same value with the same attributes as the other thing that is called information. That is a bit simplistic, but each to their own. For you, information is passed down; so biological work is societal work. I don't subscribe to that, in fact, I deny that, but you stop there and seem unable to differentiate between subtle meanings further, therefore so be it.

I won't argue against your viewpoint. Not because I agree with you, but because there is no way I can get through.

[Skepdick]

Whatever the proper expression is for "set"-ting. If it changed after a certain point in the individual's development, and kept changing 'till death, then DNA identification would be impossible. But it is not impossible.

That's a gross misunderstanding of the probabilistic nature behind any identification process, and the amount of evidence required to draw such conclusions.

All that is necessary to distinguish "you" from any other human on this planet is 33 bits of information e.g log-2(8 billion)

A strand of human DNA contains about 1.5GB of information. Even when we take into account that 99.9% of that is shared across all humans, there are still 1.5 million bits which are unique to you.

TL;DR We have 1.5 million. We need 33. Your 'impossibility' claim is 5 orders of magnitude wrong.

But I won't argue against your viewpoint, because there is no way I can get through. You don't even know who Shannon is or why my this post is directly related to his work.

[Hrvoje]

Hi Hrvoje, I'm trying to make sense more precisely of what you are getting at and see others responding with answers I agree with in parts but still not sure what you are asking.

Hi Scott, it is interesting what you wrote, and let me explain how I came up with the question, and what is it that I am asking. I was reading papers from David Deutsch, namely this:

http://constructortheory.org/portfolio/ ... or-theory/

and more specifically, this:

http://constructortheory.org/portfolio/ ... formation/

and listening to his TED interview:

https://www.stitcher.com/podcast/the-te ... e/56853300

and following his tweeter account, there he mentions different definitions of knowledge he came up with:

https://twitter.com/DavidDeutschOxf/sta ... 3483081729

So, two deep questions he is concerned with, are the nature of information, and the nature of knowledge, and I think it is worth knowing what he thinks about it, because he is one of the top living theoretical physicists in the world, known as a pioneer of quantum computing. One of definitions he considered was:

'Information that can program a programmable constructor'

That has specific meaning, in a sense that for example, a spring that is wound is able to do work based on potential energy it has, that is basically a work stored in its configuration, result of winding (or pressing it, to be more precise), that is work invested in such its state or configuration. That is also some kind of information about that system, that it has that energy, and is able to perform work, based on that. Different kind of information is stored in our brains, or for example in our DNA. Enzymes that synthesize proteins (from proteinogenic amino acids found in the surrounding area, and not from nucleotides as I wrongly wrote), use information stored in DNA in that chemical reaction in which they act as catalysts that are "programmable", so it is a different kind of ability that is based on information that is available to them. So, the question is to compare these two abilities.

[Hrvoje]

This is a fallacy of "equivocation". Information in DNA is not a program, or a changeable something. If a DNA is set, it keeps replicating itself exactly. It will produce over and over again the same functional proteins.

Have you heard of a quine

A quine is a computer program which takes no input and produces a copy of its own source code as its only output. The standard terms for these programs in the computability theory and computer science literature are "self-replicating programs", "self-reproducing programs", and "self-copying programs".

It is interesting that in a few emails that I managed to exchange with David Deutsch, in one of them he also wrote me about quines. I think that was the nearest experience of direct communication with a genius that I managed to achieve so far in my life. The point of his mentioning was somewhat different, as he shouldn't convince me about the fact that DNA is a program for these enzymes.

[Scott Mayers]

Hrvoje, I'd need a lot of time to invest in determining the value of the resources you gave me to look at. But I'm guessing that it may probably only add superfluous information for me that turns out to be unnecessary. A lot of these logic-related discussions are reinventions or reinterpretations upon the same concepts using different terms and approaches. To me, I treat static or quantized approaches (or 'finite' by math's terms) co-equally representable through a 'continuous' approach. Both are also necessary if we are to understand reality.

So, for me, I think of everything in Totality as a type of 'machine' to which the object of being scientific is to try to figure out the logic of such machines. The inputs and outputs are treated as 'static' constants (though 'variable' where indeterminate of more than one constant existing). However, the "data" these inputs and outputs represent quantitatively can also be understood as machines too. Thus we can interpret the data as also a machine that can represent change dependent upon its own relative inputs and outputs. Then too, the original machines can be thought of as 'data' relative to other machines, etc.

As to the 'constructive' factor, I believe this is related to contradictions. While we normally presume a contradiction just assures us that something is NOT true, this is naive because it can also mean that what is 'contradictory' can also mean, "look elsewhere" should it still remain 'true'. That is, we need to include a 'constructive' factor to contradiction.

Reading the abstracts of the links you gave, I cannot determine if he is treating physical reality of our own particular world as being strictly true or false. It appears that he does. Yet, 'contructive' logics EXTEND this to allow for any number of 'dimensions' of reality. Should you discover something contradictory YET still 'true' in our world, it is more likely that should it BE true of our world, it means that that 'truth' just indicates a NEW dimension. If something is contradictory but NOT of our world, it should then still be true but beyond or outside of the domain of our particular world.

Like I said, I need more time to look into your links to see if I can understand what David Deutsch is trying to UNIQUELY state.

As to genetic biology, I have to note that while DNA evolved to be a storage of data about construction, I'd recommend looking at RNA first, as this evolved first as small segments of DNA that acted as 'data' sequents used to inform how proteins are to be built. These chemicals are also machines relative to themselves that treat what it reacts with as its 'data'. So I disagree with anyone who assures us that the data itself is ONLY a catalyst. Even money, though a token data that acts as a catalyst, from its own perspective, the token is itself a machine that treats what it changes as 'data', just in 'dynamic' form.

[Hrvoje]

Please read more carefully.

Mutation does not occur after DNA is set. I am not a biochemist; but I know that if a mutation occurs then special cells or proteins hunt that mutation down and kill it. People or animals or plants don't change their DNA after it's set. Whatever the proper expression is for "set"-ting. If it changed after a certain point in the individual's development, and kept changing 'till death, then DNA identification would be impossible. But it is not impossible. So DNA does not change after a certain age has been reached by the embrio or by the individual.


It is a semantic point. "Information" is not "information". It seems I am unable to describe for you the difference. For you if one thing is called information, then it's the same value with the same attributes as the other thing that is called information. That is a bit simplistic, but each to their own. For you, information is passed down; so biological work is societal work. I don't subscribe to that, in fact, I deny that, but you stop there and seem unable to differentiate between subtle meanings further, therefore so be it.

I won't argue against your viewpoint. Not because I agree with you, but because there is no way I can get through.

I don't think that the problem here is that I am unable to grasp your subtleties, but some things that you say are not logical, and you are not sufficiently informed. If mutation does not occur, why would it need to be hunted down and killed? There are processes by which a cell identifies and corrects damage inflicted on its DNA, and if it is beyond repair, it can undergo apoptosis, that is a programmed cell death, and if that doesn't happen, it can enter an irreversible state of dormancy, known as senescence, or a state of unregulated cell division, and then it becomes a subject to hunting down and killing.
But the big question is posed by, among others, James A.Shapiro, and that is, is DNA a ROM of the cell, subject only to accidental changes, or its RW memory, that would contradict the central dogma of molecular biology?

[Scott Mayers]

Please read more carefully.

Mutation does not occur after DNA is set. I am not a biochemist; but I know that if a mutation occurs then special cells or proteins hunt that mutation down and kill it. People or animals or plants don't change their DNA after it's set. Whatever the proper expression is for "set"-ting. If it changed after a certain point in the individual's development, and kept changing 'till death, then DNA identification would be impossible. But it is not impossible. So DNA does not change after a certain age has been reached by the embrio or by the individual.


It is a semantic point. "Information" is not "information". It seems I am unable to describe for you the difference. For you if one thing is called information, then it's the same value with the same attributes as the other thing that is called information. That is a bit simplistic, but each to their own. For you, information is passed down; so biological work is societal work. I don't subscribe to that, in fact, I deny that, but you stop there and seem unable to differentiate between subtle meanings further, therefore so be it.

I won't argue against your viewpoint. Not because I agree with you, but because there is no way I can get through.

I don't think that the problem here is that I am unable to grasp your subtleties, but some things that you say are not logical, and you are not sufficiently informed. If mutation does not occur, why would it need to be hunted down and killed? There are processes by which a cell identifies and corrects damage inflicted on its DNA, and if it is beyond repair, it can undergo apoptosis, that is a programmed cell death, and if that doesn't happen, it can enter an irreversible state of dormancy, known as senescence, or a state of unregulated cell division, and then it becomes a subject to hunting down and killing.
But the big question is posed by, among others, James A.Shapiro, and that is, is DNA a ROM of the cell, subject only to accidental changes, or its RW memory, that would contradict the central dogma of molecular biology?

You appear to be questioning whether DNA as data cannot itself be alterable without mutation. While this CAN occur, DNA acts like a country's constitution. It requires being less able to be easily changed or the mechanisms of which it could be flexible to adapt to be altered with ease in an environment would make it be able to be exploited by competing lifeforms, assuring it would have a less likelihood of survival. So mutation, while not always essential for altering DNA, would be more favorable for evolution to occur where there is no predetermining controller (like a 'god' by most thinkers) to manage with care and precision not to allow changes of DNA to occur recklessly.

For '-1-', with respect to your response, mutations necessarily affect DNA normally. It is whether the DNA that gets altered is what gets into the sperm or eggs that allow for adaptive changes. But it may be possible to alter it in restricted senses by the environment. There may be a real means for DNA to also be alterable within our biology but that it is evolutionarily less probable for such mechanisms to survive a 'normal' potential.

[Skepdick]

It is interesting that in a few emails that I managed to exchange with David Deutsch, in one of them he also wrote me about quines. I think that was the nearest experience of direct communication with a genius that I managed to achieve so far in my life. The point of his mentioning was somewhat different, as he shouldn't convince me about the fact that DNA is a program for these enzymes.

You should remember that Deutch also contrived the CTD principle: The principle states that a universal computing device can simulate every physical process. . And that such a device exists in theory and in practice.

The CTD paradigm then begs the question: Is there a phenomenon that is not a physical process? If you accept causality as a fundamental principle of reality, then you would be hard-pressed to answer 'no'. A causes B is a process. And therefore subject to the CTD principle.

Obviously 'causality' goes out the window once you get to the quantum universe, but since your interest is bioinformatics, I think the classical model of information/computation will suffice for your interests.

[Scott Mayers]

It is interesting that in a few emails that I managed to exchange with David Deutsch, in one of them he also wrote me about quines. I think that was the nearest experience of direct communication with a genius that I managed to achieve so far in my life. The point of his mentioning was somewhat different, as he shouldn't convince me about the fact that DNA is a program for these enzymes.

You should remember that Deutch also contrived the CTD principle: The principle states that a universal computing device can simulate every physical process. . And that such a device exists in theory and in practice.

The CTD paradigm then begs the question: Is there a phenomenon that is not a physical process? If you accept causality as a fundamental principle of reality, then you would be hard-pressed to answer 'no'. A causes B is a process. And therefore subject to the CTD principle.

Obviously 'causality' goes out the window once you get to the quantum universe, but since your interest is bioinformatics, I think the classical model of information/computation will suffice for your interests.

He seems an interesting guy. I'm listening to him with Sam Harris at the moment and find a lot of agreement with his views. Certainly I agree with the CTD principle. I'm not sure that quantum computers can literally exist though. We can possibly prove THAT something else exists beyond our reality but not particularly what. [I take issue with Bell's Theorem being used to confirm the Copenhagen interpretation of QM.] So while we may be able to simulate machines that act as though they are in superposition (quantum computation solves multiple problems simultaneously), we may not actually be able to make such a machine. He and I agree on multi-world ideas to overcome this but the evidence that even something is remotely 'weird' as initially interpreted about quantum phenomena are themselves wanting of a more rational explanation.

[-1-]

Please read more carefully.

Mutation does not occur after DNA is set. I am not a biochemist; but I know that if a mutation occurs then special cells or proteins hunt that mutation down and kill it. People or animals or plants don't change their DNA after it's set. Whatever the proper expression is for "set"-ting. If it changed after a certain point in the individual's development, and kept changing 'till death, then DNA identification would be impossible. But it is not impossible. So DNA does not change after a certain age has been reached by the embrio or by the individual.


It is a semantic point. "Information" is not "information". It seems I am unable to describe for you the difference. For you if one thing is called information, then it's the same value with the same attributes as the other thing that is called information. That is a bit simplistic, but each to their own. For you, information is passed down; so biological work is societal work. I don't subscribe to that, in fact, I deny that, but you stop there and seem unable to differentiate between subtle meanings further, therefore so be it.

I won't argue against your viewpoint. Not because I agree with you, but because there is no way I can get through.

I don't think that the problem here is that I am unable to grasp your subtleties, but some things that you say are not logical, and you are not sufficiently informed. If mutation does not occur, why would it need to be hunted down and killed? There are processes by which a cell identifies and corrects damage inflicted on its DNA, and if it is beyond repair, it can undergo apoptosis, that is a programmed cell death, and if that doesn't happen, it can enter an irreversible state of dormancy, known as senescence, or a state of unregulated cell division, and then it becomes a subject to hunting down and killing.
But the big question is posed by, among others, James A.Shapiro, and that is, is DNA a ROM of the cell, subject only to accidental changes, or its RW memory, that would contradict the central dogma of molecular biology?

You appear to be questioning whether DNA as data cannot itself be alterable without mutation. While this CAN occur, DNA acts like a country's constitution. It requires being less able to be easily changed or the mechanisms of which it could be flexible to adapt to be altered with ease in an environment would make it be able to be exploited by competing lifeforms, assuring it would have a less likelihood of survival. So mutation, while not always essential for altering DNA, would be more favorable for evolution to occur where there is no predetermining controller (like a 'god' by most thinkers) to manage with care and precision not to allow changes of DNA to occur recklessly.

For '-1-', with respect to your response, mutations necessarily affect DNA normally. It is whether the DNA that gets altered is what gets into the sperm or eggs that allow for adaptive changes. But it may be possible to alter it in restricted senses by the environment. There may be a real means for DNA to also be alterable within our biology but that it is evolutionarily less probable for such mechanisms to survive a 'normal' potential.

Hrvoje and Scott Mayers, I may have erred in describing the behaviour of DNA in the body. I don't think I did, but then again, I have only a layman's understanding of DNA behaviour.

However, it does not take away from the fact that there is an equivocation fallacy committed by you, Hrvoje and Scott Mayers, when you declare that information is passed down in the DNA. Instructions, yes. Instruction sets, yes. Even changing instruction sets. But never information in the sense we use "information" in the social sense.

The reason DNA was brought up is that Hrvoje insisted that information is passed by DNA. I denied this, still deny it. In the social sense, information is passed over between individuals, where there is intent of the originator to pass it down. DNA is not intentional. You can't alter your own DNA by intent (until very recent times).

The question came up because Hrvoje asked what the difference was between work in physics and work in society. I explained the difference. Hrvoje came up with the objection that DNA does societal-type work, because it passes information. That's where I pointed out that it's not information in the same sense as societal information.

Then the topic got onto a tangent, and the original topic was totally buried. That being, what separates physical work from societal work. That question has been answered, and the discussion since is not meaningful to the actual topic.

I wash my hands, I think the topic was properly handled, and then it got side-tracked and now it's about DNA. A lot of misleading misinformation gets exchanged, with a lot of provocative speculation in lieu of basing the claims on solid research.

[Skepdick]

In the social sense, information is passed over between individuals.

<Insert DNA innuendo here>

But on a serious note (and said with a lot of sarsasm) NOOOO WAAAAY!!!!

You mean like Information theory or something?
Otherwise known as THE Mathematical Theory of Communication

[-1-]

In the social sense, information is passed over between individuals.

<Insert DNA innuendo here>

Skepdick, you asshole, you are not contributing, you are just mezmerized by your own incredibly huge stupidity.

You are spittifully stupid. You can't ignore the thing that belongs there, which is "intentional". Why did you just ignore that requirement?

Because, I give you three reasons, and they are all true:

1. You are ignorant and stupid.
2. You like to be a shit-disturber.
3. You argue witout reason.

And that is just the tip of the iceberg, or in your case, shitberg.

[Skepdick]

In the social sense, information is passed over between individuals.

<Insert DNA innuendo here>

Skepdick, you asshole, you are not contributing, you are just mezmerized by your own incredibly huge stupidity.

You are spittifully stupid. You can't ignore the thing that belongs there, which is "intentional". Why did you just ignore that requirement?

Because, I give you three reasons, and they are all true:

1. You are ignorant and stupid.
2. You like to be a shit-disturber.
3. You argue witout reason.

And that is just the tip of the iceberg, or in your case, shitberg.

Except that I am contributing, you dumb ignoramus.

You literally said 'information is passed over between individuals'.

You mean like Claude E Shannon's Information theory or something?
Otherwise known as THE Mathematical Theory of Communication

NOOOO WAY!!!!

[-1-]

<Insert DNA innuendo here>

Skepdick, you asshole, you are not contributing, you are just mezmerized by your own incredibly huge stupidity.

You are spittifully stupid. You can't ignore the thing that belongs there, which is "intentional". Why did you just ignore that requirement?

Because, I give you three reasons, and they are all true:

1. You are ignorant and stupid.
2. You like to be a shit-disturber.
3. You argue witout reason.

And that is just the tip of the iceberg, or in your case, shitberg.

Except that I am contributing, you dumb ignoramus.

You literally said 'information is passed over between individuals'.

You mean like Claude E Shannon's Information theory or something?
Otherwise known as THE Mathematical Theory of Communication

NOOOO WAY!!!!

Shitberg, go wipe yourself off somebody's ass.