Self-encoding systems

[Dymanic]

Originally posted by Paul C. Anagnostopoulos

But what does teleology have to do with it? There is no teleology involved in biological life

I agree. But referring to DNA as 'self-encoding' involves making a tacit teleological assumption, implying that self-replication is an explicit design feature. Using the term: 'information' involves similar assumptions, an idea Dennett expressed in Brainstorms (and one I have referred to before):

"Any time a theory builder proposes to call any event, state, structure, etc., in any system (say the brain of an organism) a signal, or message or command or otherwise endows it with content, he takes out a loan on intelligence. He implicitly posits along with his signals, messages, or commands, something that can serve as a signal-reader, message-understanderer, or commander, else his "signals" will be for naught, will decay unrecieved, uncomprehended. This loan must be repaid eventually by finding and analyzing away these readers or comprehenders; for, failing this, the theory will have among its elements unanalyzed man-analogues endowed with enough intelligence to read the signals, etc., and thus the theory will postpone answering the major question: what makes for intelligence?"

Hammegk's objection (that referring to DNA as 'self-encoding' implies an underlying sentience) seems valid, and if we seek to solve this difficulty by attributing to something sufficient intelligence to render nucleotide base sequences into 'information', we may have to make that something the entire system, rather than just the DNA (but even then, we still haven't really avoided some teleological implications).

 

[Anders]

Self-replicating proteins come ready-made in the cell in exactly the same way that mitochondria come ready-made in the cell. The mitochondria reproduce independently of the cell. When a cell divides (either through meiosis or mitosis), the existing mitochondria population is also divided among the two daughter cells. The mitochondria then reproduce in each of the daughter cells to bring their numbers up to the necessary per-cell population.

This same process applies to proteins such as prions. This is, in fact, more or less the infectious process by which mad cow disease is supposed to turn into CJD (has that link been confirmed sufficiently that I can refer to it as a 'fact,' or is it still only a hypothesis?) This is, in fact, part of how infectious prion diseases spread, and is believed also to be an important part of how stem cells divide and specialize into body cells (through prion distribution -- prions that are at least partially inherited from the mother's egg cells in the same way that mitochondria are).

Yes, but.

It is just a matter of definition.

Anyway the prion protein is encoded in a single exon of the PrP gene. However the bad prion, aggregated prion, have the peculiar function of making non aggregated prions go aggregated.

Yeah, we can call the prion theory a fact; at least it rendered a Nobel Prize.

So when it comes to show that there are self build proteins, prions are not good examples, since they still follow the central dogma of molecular biology : gene -> transcription to RNA -> translation to protein.

I think you might think that molecules that are leftovers from the original cell are in some way self-replicating. They are not. They are just not made from genes present in the current cell, but they where build in of the former cells.

 

[Anders]

You can't even define life, let alone explain it. Feel free to pretend otherwise though; I realize your worldview couldn't survive the alternative.

Well, I would say, and so would most molecular biologists and biochemists, that life is “just” a chemical process, or a billion or so of different chemical processes. We humans can think, and therefore we might think that we are somehow better than a yeast cell or a larch.

We are not though, we are just different.

Life is not a question of philosophy; it’s a question of chemistry.

We can define life as well as anything. The problem is that it still would be a definition and a meaningless one also. If we try to define life on earth we will probably have problems when we discover extraterrestrial life. ET- life would most likely not look like ours, and I’m not talking about appearance, but about molecular biology.

 

[drkitten]

So when it comes to show that there are self build proteins, prions are not good examples, since they still follow the central dogma of molecular biology : gene -> transcription to RNA -> translation to protein.

I think you might think that molecules that are leftovers from the original cell are in some way self-replicating. They are not. They are just not made from genes present in the current cell, but they where build in of the former cells.

Not necessarily; in the case of a self-replicating protein, the original gene (or enzyme) necessary to make the protein may no longer exist, as the replication function has been taken over by the prions.

Specifically, you misunderstand the role/nature of prions. Prions are not produced by RNA-transcription. Prions are alternative (and typically energetically unfavorable) topological variations of other proteins. The prion protein (the aggregated protein) is not coded genetically and will not be produced by the "normal" cellular reproduction process of gene transcription.

There have been experiments performed with artificial prions, where a "normal" cell has been deliberately "infected" with artificially produced (aggregated) variations of normal proteins, which then proceed to reproduce themselves from the normally produced cellular proteins. The host cell has no means of creating such a prion; its normal genetic reproduction mechanism cannot produce such an output. And yet, the prion self-reproduces.

It seems extremely odd to claim that the entity responsible for the prion reprodcution is the cellular gentics that demonstrably cannot reproduce the prion.

 

[Dr Adequate]

Someone asks a serious question which has something vaguely to do with evolution, so hammy has to come out with his dreary meaningless spam

Please justify your belief that dna is self-coding, other than as a demonstration of underlying sentience.

What the heck does this mean? "Other than as a demonstration of underlying sentience"? Each of those words means something seperately, and you put them together, and suddenly they don't. As we don't speak hammygibble, you'll have to speak English.

Why don't you start with the vacuum (may I say "nothing") ... get a few quarks & bosons going first.

And this is a masterly refutation of evolution... oh, sorry, my mistake, it's a complete non sequitur. Shut up, hammy, the grown-ups are talking.

You can't even define life, let alone explain it. Feel free to pretend otherwise though; I realize your worldview couldn't survive the alternative.

How many times do you have to be told a thing before you'll admit that you've been told it?

LIFE IS COMPLEX ORGANIC CHEMICALS WHICH GIVEN THE RIGHT ENVIRONMENT CAN CATALYSE THEIR OWN SYNTHESIS.

Now if you won't actually shut up, please get some fresh, original gibble and some brand new lies. Because frankly, you're becoming a bore.

 

[Anders]

Not necessarily; in the case of a self-replicating protein, the original gene (or enzyme) necessary to make the protein may no longer exist, as the replication function has been taken over by the prions.

Specifically, you misunderstand the role/nature of prions. Prions are not produced by RNA-transcription. Prions are alternative (and typically energetically unfavorable) topological variations of other proteins. The prion protein (the aggregated protein) is not coded genetically and will not be produced by the "normal" cellular reproduction process of gene transcription.

There have been experiments performed with artificial prions, where a "normal" cell has been deliberately "infected" with artificially produced (aggregated) variations of normal proteins, which then proceed to reproduce themselves from the normally produced cellular proteins. The host cell has no means of creating such a prion; its normal genetic reproduction mechanism cannot produce such an output. And yet, the prion self-reproduces.

It seems extremely odd to claim that the entity responsible for the prion reprodcution is the cellular gentics that demonstrably cannot reproduce the prion.

OK, accoding to Alberts et Al : "When proteins fold improperly, they can form aggregates that can damage cells and even whole tissues…….Prion diseases- such as scrapie…., and CJD in humans – are also caused by protein aggregates.”

So according to the book, Alberts et Al, Prions are ordinary proteins that have folded erroneous. But it has a very dangerous habit to take a properly folded Prion and make it an aggregate, thus the bad prion can propagate very quickly through tissue.

Nowhere but from you, have I seen something that suggests that prions create themselves. The Prion gene is very small so I really doubt that it has any replication domains. But I could be wrong, since I’m not a prion expert. Please enlighten me!

 

[drkitten]

OK, accoding to Alberts et Al : "When proteins fold improperly, they can form aggregates that can damage cells and even whole tissues…….Prion diseases- such as scrapie…., and CJD in humans – are also caused by protein aggregates.”

So according to the book, Alberts et Al, Prions are ordinary proteins that have folded erroneous. But it has a very dangerous habit to take a properly folded Prion and make it an aggregate, thus the bad prion can propagate very quickly through tissue.

Nowhere but from you, have I seen something that suggests that prions create themselves. The Prion gene is very small so I really doubt that it has any replication domains. But I could be wrong, since I’m not a prion expert. Please enlighten me!

I think you're missing a key aspect here. There is no such thing as a prion "gene"; a prion is formed from an "ordinary" protein by adjusting how it's folded (its topology, if you will). The genome codes only for the amino acid sequence. The prion and the ordinary protein are identical in chemical composition and are therefore coded by the same genes.

Protein folding is to some extent a stochastic process; a protein might (in fact, is likely to) fold "correctly" and produce a normal protein, or might fold wrongly and produce a variant we call a prion. (The phrase "properly folded prion" is a little odd here -- a properly folded prion is, almost by definition, a normal protein).

What really makes a prion special, however, is its chemical activity. Chemical activity among proteins is a function both of composition and of shape -- a differently folded protein will have a different chemical effect. (No surprises here; graphite and diamond also have different chemical effects.) The chemical effects of proteins is what lets enzymes do their work -- they act as catalysts to make other chemical reactions happen on the basis of the shape they have folded into.

A prion is simply a (protein) enzyme whose effect is to autocatalyze. It will take "normal" examples of its own proteins and catalyze them to change shape.

Just type "prion" and "autocatalysis" into your favorite web browser and you'll find lots of highly technical information. A good starting paper is Autocatalysis, Information, and Coding, which has a section on prion reproduction in exactly this context (section 2 at the bottom of the second page). Quoting from this section:

The infectious, replicating entity responsible for the transmission of prion disease is now believed to be no more than a stable conformational state of PrP [emphasis mine].... According to the Central Dogma [...] the information specifying stable phenotypic differences between similar entities much be encoded in nucleic acid genes. But such is not the case. The existence of prions demans that we generalize our notions of how biological information is stored.

Interesting paper. Actually, almost everying the Santa Fe Institute does is interesting.....

 

[TillEulenspiegel]

Paul:
"Are there any examples of self-encoding systems in nature besides DNA?"


Ok going out on a long branch here so don't jump too hard.
How about Fractals? Mandelbrot sets? The quality of these maths are both self encoding and self-replicating.It is math tho...........

No? To far from nature? How about the sun and other bodies like it? They are composed of the remnants of other long dead stars and altho different in certain quantities obey the same rulesets. The solar system model is not as rare as we once thought.

As far as the DNA/life question hammegk tries to raise , conversely what about viruses? They are not technically “alive” yet they replicate their DNA!?

Crystals were raised and are an example. Some new experiments have synthesized DNA and Amino acids and even proteins by tRNA synthetase . So it depends on the avenue of inquiry that determines the answer. If your asking are there processes that are similar to the DNA molecule which engender life on a chemical basis, except for prions I would say no. If the question is open ended then , yes there are a few examples of self-encoding ,replicating behavior.


As an aside :The first experience I ever had with AI was a sim called "Life". They were Programed automata that feed from the environment and multiplied into a different automata's territory, where the two would strive for dominance. Like fractals simple ruleset , complex behavior.

 

[Paul C. Anagnostopoulos]

Dymanic said:
I agree. But referring to DNA as 'self-encoding' involves making a tacit teleological assumption, implying that self-replication is an explicit design feature. Using the term: 'information' involves similar assumptions, an idea Dennett expressed in Brainstorms (and one I have referred to before):

I see no reason why the term self-encoding should have any teleological implications, but I'm happy to use another word that describes how life works.

Any time a theory builder proposes to call any event, state, structure, etc., in any system (say the brain of an organism) a signal, or message or command or otherwise endows it with content, he takes out a loan on intelligence. He implicitly posits along with his signals, messages, or commands, something that can serve as a signal-reader, message-understanderer, or commander, else his "signals" will be for naught, will decay unrecieved, uncomprehended. This loan must be repaid eventually by finding and analyzing away these readers or comprehenders; for, failing this, the theory will have among its elements unanalyzed man-analogues endowed with enough intelligence to read the signals, etc., and thus the theory will postpone answering the major question: what makes for intelligence?

We understand what the message-understanderer is in the case of DNA, so I don't think this is a problem.

~~ Paul

 

[hammegk]

Someone asks a serious question which has something vaguely to do with evolution, so hammy has to come out with his dreary meaningless spam

What the heck does this mean? "Other than as a demonstration of underlying sentience"? Each of those words means something seperately, and you put them together, and suddenly they don't. As we don't speak hammygibble, you'll have to speak English.

And this is a masterly refutation of evolution... oh, sorry, my mistake, it's a complete non sequitur. Shut up, hammy, the grown-ups are talking.

How many times do you have to be told a thing before you'll admit that you've been told it?

LIFE IS COMPLEX ORGANIC CHEMICALS WHICH GIVEN THE RIGHT ENVIRONMENT CAN CATALYSE THEIR OWN SYNTHESIS.

Now if you won't actually shut up, please get some fresh, original gibble and some brand new lies. Because frankly, you're becoming a bore.

Unlike the blathering and meaningless diatribes of yours -- see sample above. You, WoTS, & Bill sure do think alike.

 

[Dymanic]

Originally posted by Paul C. Anagnostopoulos

I see no reason why the term self-encoding should have any teleological implications, but I'm happy to use another word that describes how life works.

I don't necessarily have any more problem with referring to DNA as 'self-encoding' than I do with referring to a storm cloud as 'angry', unless the focus is on the mechanics of the way emotion is expressed in weather, and on a search for similar expressions of emotion in other natural phenomena. But at that point, the underlying assumptions do begin to bother me.

We understand what the message-understanderer is in the case of DNA, so I don't think this is a problem.

Well, we understand what the message transcriber is -- but that's not the same thing. If we accept transcription as the point where 'meaning' is extracted from the DNA, we are accepting that meaning to be merely: "this amino acid here, at this time" (or: "this protein here, at this time") -- and we have just abandoned the idea of DNA being 'self encoding'. To justify that distinction, we must make a much stronger inference, something like: "this amino acid here, at this time, because doing so will favor the creation of more copies of these instructions". There is a difference between a storm cloud acting angry and a storm cloud being angry. See what I mean?

I don't know if there is another word describing how life works, but I'd look for something that expresses the idea that replication is something that sort of just happens to DNA - but only sometimes, and even then as much by virtue of it being acted upon by other elements within a system as of it acting on them. (If there is such a word, it will most likely be in German, and have lots of syllables).

 

[Paul C. Anagnostopoulos]

Dymanic said:
I don't necessarily have any more problem with referring to DNA as 'self-encoding' than I do with referring to a storm cloud as 'angry', unless the focus is on the mechanics of the way emotion is expressed in weather, and on a search for similar expressions of emotion in other natural phenomena. But at that point, the underlying assumptions do begin to bother me.

Sorry, I just don't understand your objection. DNA encodes all the internal mechanisms of the cell, including the ability to code and decode DNA itself. Therefore it is "self-encoding." I see no reason why we have to attribute all sorts of emotional nonsense to the word self.

Well, we understand what the message transcriber is -- but that's not the same thing. If we accept transcription as the point where 'meaning' is extracted from the DNA, we are accepting that meaning to be merely: "this amino acid here, at this time" (or: "this protein here, at this time") -- and we have just abandoned the idea of DNA being 'self encoding'.

How so? Well, actually, I see part of the problem. I didn't mean to suggest that DNA alone is self-encoding. I thought I clarified that up above.

To justify that distinction, we must make a much stronger inference, something like: "this amino acid here, at this time, because doing so will favor the creation of more copies of these instructions". There is a difference between a storm cloud acting angry and a storm cloud being angry. See what I mean?

Not really. Seems like wordplay born of descending into philosophy when science was the intent.

~~ Paul

 

[Dymanic]

Originally posted by Paul C. Anagnostopoulos


Seems like wordplay born of descending into philosophy when science was the intent.

I plead guilty; but with an excuse: I think your initial premise takes some philosophical baggage on board unexamined -- no, worse than that; it is based on interpretation of scientific observations within an unexamined philosophical framework. (Happens all the time). But I've said my piece, and I won't flog the thread any further.

As for your opening question: I can't think of any, but I'll keep an eye peeled, and if I spot something that looks like it might qualify, I'll get back to you.

 

[hammegk]

Not really. Seems like wordplay born of descending into philosophy when science was the intent.

"Science" certainly works better when it doesn't question too deep. You say 'truth', I say superficiality.

At least Dr.A has assured us life is carbon based.

 

[Dr Adequate]

Unlike the blathering and meaningless diatribes of yours -- see sample above. You, WoTS, & Bill sure do think alike.

Would anyone else who didn't understand my post please say so?

Anyone else find it "meaningless"?

Or is it just hammy who's too moronic to understand plain English?

Which bits are you too stupid to understand?

There are lots of people here who will help you with those long, difficult words.

But I'm wondering... if you're functionally illiterate, as you claim, why do you spend so much time posting on these forums?

 

[Dr Adequate]

At least Dr.A has assured us life is carbon based.

So... when you claimed to find no meaning in my post, you were in fact lying. Thanks for clearing that up.

 

[Anders]

I think you're missing a key aspect here. There is no such thing as a prion "gene"; a prion is formed from an "ordinary" protein by adjusting how it's folded (its topology, if you will). The genome codes only for the amino acid sequence. The prion and the ordinary protein are identical in chemical composition and are therefore coded by the same genes.

Protein folding is to some extent a stochastic process; a protein might (in fact, is likely to) fold "correctly" and produce a normal protein, or might fold wrongly and produce a variant we call a prion. (The phrase "properly folded prion" is a little odd here -- a properly folded prion is, almost by definition, a normal protein).

What really makes a prion special, however, is its chemical activity. Chemical activity among proteins is a function both of composition and of shape -- a differently folded protein will have a different chemical effect. (No surprises here; graphite and diamond also have different chemical effects.) The chemical effects of proteins is what lets enzymes do their work -- they act as catalysts to make other chemical reactions happen on the basis of the shape they have folded into.

A prion is simply a (protein) enzyme whose effect is to autocatalyze. It will take "normal" examples of its own proteins and catalyze them to change shape.

Just type "prion" and "autocatalysis" into your favorite web browser and you'll find lots of highly technical information. A good starting paper is Autocatalysis, Information, and Coding, which has a section on prion reproduction in exactly this context (section 2 at the bottom of the second page). Quoting from this section:



Interesting paper. Actually, almost everying the Santa Fe Institute does is interesting.....

Thanks for the lecture doctor! I personally of course know all this, as the molecular biologist to be I am. But I don't agree with the statement that the folding is stochastic. It's not. Most if not all, of the function of the proteim lies on the form of the protein/enzym. The folding usually is done so the protein forms a folding where it has it's lowest energy level, and of course that the polar/nonpolar sidechains are outwards/inwards, and that M and C residues form bi-sulfid binds, etc, etc.

So we aggree that a prion is a missfolded protein that makes it quite dangerous? I say, which you don't agree with, that the prion is a protein from from a gene, named PrP, which is folded wrongly. And that the gene, PrP, of wich there are many, produce both sorts, both the correctly folded and the miss folded.

Miss folded protein is nothing new or unique to prions. All proteins are miss folded now and then, but they are talking care of by cleaner proteins, before they can do harm. Prions do seem to elude that safeguard somehow.

Anyways, I think we mean the same thing, just different wording, perhaps different textbooks at the university.

 

[hammegk]

Dear Dr.A:

Was I lying? Nah.

I found your spew as "meaningful" (implication: something new, unknown, interesting) as any recital of abc's by a 6 year old.

The kitten-Anders exchange had a bit of meat. Are prions "life"? How do you know?

 

[Peskanov]

Are there any examples of self-encoding systems in nature besides DNA?

Fascinating question; I can only think of crystals (especially snowflakes) as candidates, but I see this has been pointed already.
Of course now we have artificial self-encoding systems, mostly computer programs.

 

[hammegk]

Peskanov

You bare the problem both with 'self-coding code' which needed a programmer to set in motion on pre-existing hardware, and with the fact that crystallization is a demo of pre-existing laws-of-physics coding, also operating on an existing substrate.