Paul C. Anagnostopoulos
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Are there any examples of self-encoding systems in nature besides DNA?
~~ Paul
~~ Paul
Self-encoding systems
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Paul C. Anagnostopoulos
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I'm thinking about something that has an information store that encodes part or all of the structure of the thing itself.
~~ Paul
~~ Paul
I share hammegk's reservations. I was once happy to refer to DNA as a self-replicating molecule (self-encoding, whatever), but I have come to view this as hopelessly oversimplified and teleologically loaded. It's not just that the process by which a DNA molecule is replicated is indirect, implicit, convoluted and many-leveled -- it's that the bulk of the 'information store' to which you refer does not actually reside with the DNA itself, but with the cell, the organism, the environment, the history of the organism and its predecessors and their interactions with their environments and of their cells' interactions with the DNA, etc.
I suppose that by: "in nature", you mean to exclude meme-space?
I suppose that by: "in nature", you mean to exclude meme-space?
I do not share hammegk's reservations. The DNA molecule is perhaps not self-replicating, but it is a fact that all proteins needed for the replication does at some point start as a gene in a DNA molecule. There is no information store in the cell that doesn’t originate from the DNA molecule. There is however one more store within the cell that holds DNA molecules, the mitochondria.Dymanic said:
The bulk of the information is indeed in the DNA molecules, but not in the genes, but still in the DNA molecule. The cell don’t really care about the environment, but it does react on signals, other molecules that come swimming in the cells vicinity. The history of the organism is not stored anywhere however, just as antibodies.
I do understand the question from Paul, and my answer would be a big fat NO. Ta bad though, because if makes it harder to prove evolution. I would be nice if someone could dig up a cell, which still uses RNA as information carrier, as it is thought that the first cells did.
And I also don’t think we should make this a philosophy question, but keep it as a science question. We know enough science to explain a great deal about life.
Of course, that is fundamentally true of any type of information. Only a part of the meaning is in the message; the rest is in the receiver. The message (DNA in this case) is just one component of a complex system.
But the concept of information is still useful, because there are various ways to separate the effects of the different components in an information system, for example by holding some of them as constant as possible (just like any other area of science). Consider what would happen if you replaced the DNA in a fertilised mouse egg with the DNA from an elephant. If you got anything at all, it would be more like an elephant than a mouse. This gives an idea how we might begin to quantify the proportion of information held in the DNA as opposed to the rest of the cell.
I would say that the word ‘systems’ in the original question is a bit misleading. DNA is more analogous to the message component than to the whole system. I think the question is about messages that, given the rest of the system, preferentially reproduce themselves rather than a potential rival message of the same type. Fire would therefore not qualify. But crystals certainly would. And see Seven Clues to the Origin of Life by Graham Cairns-Smith for a possible connection between crystals and DNA.
I'm not sure I follow you there.
Can't say I agree with that. The specific proteins produced by a cell at a particular time can be affected by a number of environmental factors such as temperature, light, chemicals absorbed from food or through the skin or produced by the body in response to environmental stimuli...
There ya go.
Oops.
Paul C. Anagnostopoulos
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Give me a break. I said self-encoding, not self-actualizing.
Come on, people, I'm not asking a philosophical question here. Anyway, how does the information reside anywhere but in the DNA and possibly a few other places in the cell? There is no organism at the beginning of its life, its predecessors are all dead, and the environment contributes pressure but not structural information (except for occasional transfers). Let's not confuse the information with the source of the information.
I'm simply wondering if there is anything else like the DNA world, where some sort of store contains information that encodes the structure of the object containing the store, to one extent or another.
Perhaps if there was, it would have competed with the DNA world and lost.
~~ Paul
I think you are, actually.
You make it sound like a naked DNA strand, floating free in empty space, would contain all the information necessary to produce a complete organism if only it were lucky enough to land in some place where all the requisite raw materials were available -- but there IS an organism at the beginning of a life.
The popular description of the DNA as 'the blueprint' is misleading. It's more like 'the list of ingredients'. From the very moment of conception, the chemistry of the cell provides the context within which the determination is made as to what ingredient will be added next (the cell's location providing the 'where) -- and the environment in turn provides the context within which that chemistry is determined.
Whoo boy, I'm afraid you have just popped the lid off quite a can of worms. This is the teleological aspect I spoke of, and I don't see how one could possibly hope to begin to explore it without deciding on a philosophical framework (deciding not to use a philosophical framework is a philosophical framework, btw). If you're not up for that, I understand; I'm not sure I am either. But pretending that it is all just drop-dead simple may not be very productive.
It's possible to explain a lot about a thing without first having decided whether to call it "alive" or "dead".
If it turns out, after examining how things actually work, that the distinction is simply a vague, though often useful, convention, but not at all fundamental, then so be it.
Anders said:
I don't believe this is a "fact," as it ignores the existence of prions and other such methods of protein fabrication. There are demonstrably a number of proteins floating around that have been created from other proteins by other proteins with out a direct genetic precursor; not all of these have known function, and I would
be surprised to see that such a widespread and common method had not been adapted into reproduction.
Paul C. Anagnostopoulos said:
Dawkins addressed this quite extensively in The Ancestor's Tale, and it would be a disservice both to his knowledge and to his writing skill to attempt to reproduce his entire argument here. But, basically,.... no. The environment contributes structural information as well as pressure, and the reproductive process is designed to take advantage of these pressures.
A little-known fact about genetics is that reptiles usually have a much larger and more complicated genome than mammals. The reason for this is that the conditions under which an egg will develop are much more variable than the conditions under which a fetus will. For example, there will typically be serveral alternative genes (or alternate ways of expressing a gene as a protein) that are temperature dependent. For example, if the temperature is less than 20 degrees, protein A will be formed. For temperatures between 20 and 25, protein B will be formed, and above 25, a third protein C will be formed.
A macro-scale of this effect is the variation of sex with temperature in alligators and turtles. At low temperatures, turtles develop testes (and are male). At high temperatures, turtles develop ovaries (and are female). At intermediate temperatures, genetics dominates. There are known enzymes that will convert oestrogen to testosterone and vice versa. The same genome will produce a different organism in a different chemical environment, but the chemical environment itself is temperature-dependent.
In mammals, this is much less of an issue, because the mother controls the environment much more closely. But this implies that the information for creating a mammal (such as the temperature at which the embryo must be held) is not in the DNA of the developing organism, but in the mother. In other words, there is another, extra-genetic source of necesary information.
Prions, as I mentioned, are another demonstrated source of non-genetic information. Ribozymes (RNA-based enzymes) provide another kind of non-genetic enzymes. They're not DNA, but they're necessary for organism reproduction.
Don't we call these "crystals"? I can control the structure of a large crystal by using a seed crystal with a specified structure. The crystal "grows" by coopting atoms from the growth medium; this is why snowflakes, for example, have their characteristic hexagonal symmetry. The "store" is simply a subpart of a crystal, which is replicated endlessly throughout the entire crystal.
Paul C. Anagnostopoulos
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When I asked whether there was anything else that was self-encoding, I wasn't suggesting that it had to be nakedly self-encoding. Of course there is machinery with it to encode and decode it. The cool thing is that the DNA encodes everything, including the encode/decode machinery.
Did I say it was simple? But what does teleology have to do with it? There is no teleology involved in biological life.
Okay, I was oversimplifying the contribution of the environment. Clearly the developing organism and the environment have a "symbiotic" relationship. This would be the case with any other self-encoding system we might find.
I started The Ancestor's Tale before TAM, but I've been sidetracked since. Can't wait to get back to it.
This is a good example. Now let's compare crystals to life. Is there some fundamental aspect of the coding/decoding process in DNA that does not exist in a crystal?
~~ Paul
Anders said:
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).