DNA and the 'Code of Life'

@pagan,

pagan;119370 wrote:

do you therefore think that the information in dna/rna molecules is potentially medium dependent? ie when abstracted into a genome sequence and printed onto paper the information is predictive in the hands and minds of scientists. By contrast, when the information is materialised specifically in dna/rna molecules (not paper), it is physically formative and life creating.

There is a difference between the two, but this is a matter of scientific accuracy and not one of metaphysics.

What is predicted by scientists is meant to be as close as possible to what actually is produced by that gene -- but this is a matter of reconstruction and it may not be perfect.

Let's say for instance that they complete the sequencing of the alpaca genome. There is one gene that they have a sequence for. They know it's a 'gene' because it has a promoter sequence and a termination sequence. They determine that this gene has 99% homology with a similar gene found in camels and llamas, which are close relatives, and this gene is known in those animals to produce a pancreatic digestive enzyme. The nucleotide sequence will give you the secondary sequence of the polypeptide -- i.e. you can accurately predict the sequence of amino acids. You know that the sequence will produce certain tertiary (three-dimensional) structures in a folded protein, including an alpha-helix, a beta-pleated sheet, and a serine protease active site. You know that there are signals that will deliver it to endoplasmic reticulum, and therefore you may be able to infer that it is secreted. These are all pretty important predictors, and they may all be spot on descriptions of what the ACTUAL gene product does -- but in the end the gene product just is what it is.

I did research on a gene family in malaria which includes two genes that are nearly identical (they are duplications of one another), but one version of the gene is not actually expressed (no mRNA, no protein) -- so the predicted structure of the nonfunctional gene's product is accurate except for the fact that such a gene product is never actually seen.

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@xris,

xris;119387 wrote:

The formula for life is not written down,

All life has a genetic code that we can read. Non-Life does not have a code. The genetic code is the only thing separating Life from Non-Life.

xris;119387 wrote:

if you have it, give to me, please.

You already have a copy of your very own. A 6 billion letter code in ever cell of your body. That code says "Xris", and it said "Xris" before "Xris" ever existed. It was authored within hours of your conception, and it pre-defined you before you were you.

xris;119387 wrote:

Science for years has been trying to replicate life without any success.

Replicating code is not the only requirement for life. There must be a mechanism to process the information into physicality. That mechanism is RNA.

xris;119387 wrote:

What this DNA informs you of, is the eventual outcome of evolution not the initial formula that instigated life and gave it the potential.

Yes, science is indeed finding that pseudogenes can represent a historical record of evolution. Primate olfactory genes have been discovered in human pseudogenes. But that's only one attribute. DNA also represents how to assemble the current life form. It is species specific instructions for life in the present, not just a legacy filing system.

xris;119387 wrote:

The formula for life is hidden from man, its not discovered.

Hidden implies a hider. DNA wasn't hidden any more than brainwaves were hidden, or electromagnetism, or Neptune. Watson and Crick discovered DNA just like Johann Gottfried Galle discovered Neptune, Hans Christian Orsted discovered electromagnetism, and Richard Caton discovered brainwaves (or was it Hans Berger?).

xris;119387 wrote:

Paley's watch needs more than plans it needs the concept of time to be accepted first.

You're missing the point of Paley's watch argument. It's simply representative of any object that is commonly accepted as being designed, but Dawkins says could have arisen by the cause/effect of chaos (given enough time). It could have been a toaster or a 747 aircraft. Paley's watch argument has nothing to do with the concept of "time keeping" of the watch. Only the "time and matter resources" available to hypothesize its likelihood of arising by chance.

xris;119387 wrote:

You are looking at the result not the cause.

That's often what science does. That's often the only thing that science can observe, the results. That observation of result is a primary motivator to hypothesize a cause and run experiments to test it.

xris;119387 wrote:

That initial spark of life had concealed in its make up all the future of life's venture, it had determination and a desire to succeed. There is no chaos in the cosmos its determined.

Is this your opinion, or is there empirical evidence to support your claim?

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@QuinticNon,

QuinticNon;119414 wrote:

Non-Life does not have a code.

Except for viruses, which are non-life but are self-replicating entities that have nucleic acid codes (and not all are DNA). And prions, which are self-replicating polypeptides.

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@Aedes,

Aedes;119422 wrote:

Except for...

Yes of course. Thank you.

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@QuinticNon,

There appears a misunderstanding that i dont think Im capable of curing. Imaging before life became possible in that primeval soup? There being no life, no plant life no biological semblance of life. Can you imagine that at a certain point in this endless primeval world, when we see the glimmer of life. It is quit simple but it has the ability to self generate and secure sustenance. Now did this life happen by the action of chaos theory or did it occur when we had certain elements in the correct conditions? These components that experiencing certain conditions resulting in life, can they be listed can the circumstances be recorded. If we record this event we would say this is the formula that gave us life. I dont think chaos gave us this formula, i believe it always existed in principle, it just needed endless time to find the conditions right.

If you could examine this first life would it have the code of life that told us of its determination, its ability to evolve. Is this first life complex or is it in its simplicity still capable complexity? This is where I see an engineer, this event was foreseen by the formula , although simple in it origin, still knew by determination it would succeed and reach perfection.

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@jeeprs,

But on second thought, as we want to be very specific...

Early you (Aedes) argued that DNA was not "actually" a code at all but more analogous to a template or a blueprint. I take it from your comment that you do indeed accept that DNA is a genuine code. The virus (some) and prions would be more template/blueprint than code. There is replication, but no specific probability space A being mapped to probability space B.

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@Aedes,

Aedes;119422 wrote:

Except for viruses, which are non-life but are self-replicating entities that have nucleic acid codes (and not all are DNA). And prions, which are self-replicating polypeptides.

Is there idea of what came first Aedes. Did one develop from the other or did they appear independently?

1 Reply

@xris,

xris;119428 wrote:

There appears a misunderstanding that i dont think Im capable of curing. Imaging before life became possible in that primeval soup? There being no life, no plant life no biological semblance of life. Can you imagine that at a certain point in this endless primeval world, when we see the glimmer of life. It is quit simple but it has the ability to self generate and secure sustenance. Now did this life happen by the action of chaos theory or did it occur when we had certain elements in the correct conditions? These components that experiencing certain conditions resulting in life, can they be listed can the circumstances be recorded. If we record this event we would say this is the formula that gave us life. I dont think chaos gave us this formula, i believe it always existed in principle, it just needed endless time to find the conditions right.

If you could examine this first life would it have the code of life that told us of its determination, its ability to evolve. Is this first life complex or is it in its simplicity still capable complexity? This is where I see an engineer, this event was foreseen by the formula , although simple in it origin, still knew by determination it would succeed and reach perfection.

I can see the problem you are wresting with. What if you said, given the conditions, and the right ingredients, proto-life-forms would begin to emerge on the early planet?

So here is one question: acknowledging the fact that natural selection became operative when the first life-forms emerged, how could this principle have applied to non-living forms? If it is correct that life bootstrapped itself into existence, then presumably natural selection must have been operative prior to the emergence of life.

In which case it looks awfully like a metaphysical principle rather than a natural law.

1 Reply

@xris,

xris;119428 wrote:

Can you imagine that at a certain point in this endless primeval world, when we see the glimmer of life.

Yes. That point is the exact moment when a fully codified communication protocol was engaged with matter capable of replication.

xris;119428 wrote:

It is quit simple but it has the ability to self generate and secure sustenance.

That ability is programmed... with codified information.

xris;119428 wrote:

did this life happen by the action of chaos theory or did it occur when we had certain elements in the correct conditions?

Chaos has never been demonstrated to author codified information. Life requires codified information. Having "certain elements in the correct conditions" is the act of codifying information. It's the same exact thing as saying - "e" "p" "f" "r" "c" "e" "i" "t" "n" "o" are "certain elements" that in the "correct conditions" spell "perfection". The "certain elements" are letters (ATCG) and the "correct conditions" are the arrangement of their specific codified information... "perfection".

But other "certain elements" and "correct conditions" must be present at the exact same time. It's more than just information. It's the alphabet A mapped to alphabet B, transmitter, receiver, error correction, noise reduction, redundancy, syntax, semantics... a full blown communication system must be in place at the exact same time.

Getting a code to assemble by chance is hard enough... in fact it's never been shown possible. But getting a full communication system in place at the exact same time is really the epitome of incredulity. There is no reason to believe it could ever possibly happen by chance (or probability).

xris;119428 wrote:

If we record this event we would say this is the formula that gave us life.

Recording Information is not the same thing as Authoring Information.

xris;119428 wrote:

i believe it always existed in principle, it just needed endless time to find the conditions right.

Time + Chance + Chaos has never been demonstrated as a mechanism for authorship... never.

xris;119428 wrote:

If you could examine this first life would it have the code of life that told us of its determination, its ability to evolve.

Well that's one of the great questions. We don't really know what form that first life was... DNA or RNA.

xris;119428 wrote:

Is this first life complex or is it in its simplicity still capable complexity?

We need to examine what is meant by "complex" or "simplicity". There are many primitive life forms with a genetic code 100 times the size of humans. Human code isn't that much different that a grape.

xris;119428 wrote:

This is where I see an engineer, this event was foreseen by the formula...

Engineers author formulas expressing the foresight of the engineer. Formulas cannot foresee. They can only foretell.

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@jeeprs,

jeeprs;119435 wrote:

I can see the problem you are wresting with. What if you said, given the conditions, and the right ingredients, proto-life-forms would begin to emerge on the early planet?

So here is one question: acknowledging the fact that natural selection became operative when the first life-forms emerged, how could this principle have applied to non-living forms? If it is correct that life bootstrapped itself into existence, then presumably natural selection must have been operative prior to the emergence of life.

In which case it looks awfully like a metaphysical principle rather than a natural law.

At last someone is starting to comprehend my question. The simplest life that appeared may have a code that describes it but not the theory or the explaination of how it was formed or how it has the ability to perform natural selection. It, as you say must have been theoretically possible before life appeared. You cant say one day its not possible and tomorrow it is.

This originality question, if it has always been possible and we have these constant events with causes, then lfe has always existed because if its possible, then the laws of time will say it will occur again and again. Is this just as questionable as the first event without a cause? I believe it was conceived.

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@xris,

xris;119431 wrote:

Is there idea of what came first Aedes. Did one develop from the other or did they appear independently?

Some people think that viruses arose through evolutionary events that were independent and separate from the one that produced cells. It makes a lot of sense -- clearly viruses require cells to survive. But clearly having a double stranded RNA genome is really weird, and it's thought that the advent of DNA as the main nucleic acid happened later on in early evolution.

QuinticNon;119429 wrote:

Early you (Aedes) argued that DNA was not "actually" a code at all but more analogous to a template or a blueprint. I take it from your comment that you do indeed accept that DNA is a genuine code.

QuinticNon, please understand what my real objection is:

Jeeprs and your tact is to decide which label fits DNA, then to philosophically analyze the meaning of the label.

I think that that is a logically flawed project because DNA is unique.

In some ways I agree that DNA fits the description of a code, but that doesn't mean that it should be regarded in the same way as human codes like morse code and braille.

I also feel like "code" in most contexts refers to human inventions. DNA is not a human invention. But that doesn't by any stretch require it to have a nonhuman author -- I have yet to see an argument that proves that a naturally occurring code is beyond all possibility.

QuinticNon;119429 wrote:

The virus (some) and prions would be more template/blueprint than code.

Viruses use nucleic acids in the exact same way as living things. They replicate, they are transcribed, and their transcription products encode proteins. In some cases they have their own polymeraseses, as in HIV (which famously has reverse transcriptase), in other cases they use the machinery of the host cell; in all cases they are translated by the host cell's ribosomes.

Prions are truly just template -- they are polypeptides that are encoded by host genes -- but they have an abnormal conformation that induces the host's 'normal' version to reconform into the abnormal, pathogenic one.

QuinticNon;119429 wrote:

There is replication, but no specific probability space A being mapped to probability space B.

Again, viruses use DNA and RNA in essentially the same way as any living thing. They're weird, because some have single stranded DNA genomes, some have single stranded RNA genomes, and some have double stranded RNA genomes. Some are positive-sense and some are negative-sense. But be that as it may, the same thing happens as in cells.

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@Aedes,

Aedes;119447 wrote:

I have yet to see an argument that proves that a naturally occurring code is beyond all possibility.

Even if this is true, the fact that nature has engendered codes, as distinct from just patterns, suggests to me that the attempt to understand nature in physical terms is what might need to be revised. In other words, there is another layer of complexity in nature itself over an above the interaction of entities. If nature is lawful in terms of the production and regulation of information, it indicates a higher level of order than that which can be derived from physics and chemistry, doesn't it?

1 Reply

@Aedes,

Whats natural Aedes? the idea that life can self generate from a pond when it recognises life can be sustained ? That it has this enormous unbelievable ability to evolve and examine its own creation? Whats natural?

1 Reply

@jeeprs,

The supernatural origins of life are thought to have been rejected. But I wonder if we know enough about nature to know what is 'super' to it?

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@xris,

xris;119450 wrote:

Whats natural?

I know your Q was directed at Aedes, but I must interject my own personal insight.

What is natural, is anything without a code.

Anything with a code is artificial. Yes, humans and all life are artificial, as in... authored into existence from the mind of another sentient entity.

There is no such thing as SuperNatural. There is only Natural and Artificial.

---------- Post added 01-12-2010 at 04:04 PM ----------

Yet, I could be swayed to give a title of SuperNatural to the original Unauthored Author... (be that an Author or Chaos either way)

---------- Post added 01-12-2010 at 04:10 PM ----------

HA! Imagine... If Chaos is the Author of Life... Then Chaos itself is SuperNatural.

Who Knew?

1 Reply

@jeeprs,

jeeprs;119449 wrote:

the attempt to understand nature in physical terms is what might need to be revised. In other words, there is another layer of complexity in nature itself over an above the interaction of entities.

Leave the former to the scientists and the latter to those who are interested in metaphysical speculation. And practice what you preach -- if you think that science cannot penetrate the domain of these "other terms", then you'd be wise to respect that these "other terms" cannot penetrate the domain of science.

---------- Post added 01-12-2010 at 05:18 PM ----------

xris;119450 wrote:

Whats natural Aedes?

Natural as distinct from the products of human creativity and industriousness. Yes, humans are natural in a different sense, but there is a distinction between what "occurs" in nature on its own and what a human does.

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@jeeprs,

Remember what 'nature' is taken to be, by physical scientists. Basically it is held to be 'matter in motion'. The effort is always to explain everything that can be seen in those terms. The basic ontology of the physical sciences is that matter is the enduring reality.

If nature has a heirarchy of levels, in other words, if there is an 'information' level which cannot be meaningfully comprehended in terms of the physical level, then it is a completely different model. It is exactly similar to the 'network stack' in computer technology, which describes the different layers of a communications network. The bottom layer is 'the physical layer' which provides the means of transmission - fibre-optics, ethernet, wireless and so on. But all the really interesting stuff, the content, for which the network has actually been built, exists on the higher layers - the presentation and application layers.

Nobody would try and understand the world wide web from the viewpoint of the physical layer (unless you were a Cisco engineer). Yet that is what the materialist analysis of life is analagous to.

---------- Post added 01-13-2010 at 09:23 AM ----------

and maybe this is not 'mtaphysical speculation' - perhaps it is just a different model for the world we live in.

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@jeeprs,

jeeprs;119471 wrote:

perhaps it is just a different model for the world we live in.

Yup... All that...:a-ok:

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@jeeprs,

Aedes

Quote:
Originally Posted by pagan
do you therefore think that the information in dna/rna molecules is potentially medium dependent? ie when abstracted into a genome sequence and printed onto paper the information is predictive in the hands and minds of scientists. By contrast, when the information is materialised specifically in dna/rna molecules (not paper), it is physically formative and life creating.

Quote:

Aedes

There is a difference between the two, but this is a matter of scientific accuracy and not one of metaphysics.

What is predicted by scientists is meant to be as close as possible to what actually is produced by that gene -- but this is a matter of reconstruction and it may not be perfect.

well it depends if you think that major shifts in science have metaphysical implications.

eg relativity destroyed the metaphysical possibility of absolute space and time seperate measurements in an instant. Prior to that it was up for debate. QM probability functions in the modelling likewise had major philosophical consequences re determinism.

What i am pointing out is that the genetic information abstracted into a model is now concievably media dependent. When it came to 'dead' (non information) matter, the scientific model was restricted, it was thought, by the modelling of forces and the interelationships between 'dead' matter components. With 'information matter' at the molecular level (and therefore QM level), it is quite concievable that the dead matter (dna/rna molecule) modelling of the medium, plus the modelling of the seperated information (genome), disengages a crucial aspect of its behaviour through the abstraction. The reason being that the abstracted model encodes the information (and the abstracted medium) into new a medium. eg computer circuits.

Now i realise that this does not necessarily follow, but if information is a new level of universal concept (like spacetime, momentum, charge etc) simultaneously written on to the physical level, then it is quite concievable that there is a relationship between information and a medium. This would compare to a computer circuit whereby in theory you could scale the whole thing up with string and baked bean cans and a set of rules for how they shake, and the information would not lose its formative abilities (ie calculation).

Compare to QM processing of information. If dna/rna uses QM information processing, then scaling up is not permitted conceptually without loss, because real QM processes are scale dependent. QM interacting molecules are also not classical logic dependent by definition, which is another thing that is lost by abstracting a model into a present day computer. Classical logic is not scale up dependent upon the medium that enables it to function. By contrast it is scale down dependent since at very small scales QM takes over any potential medium for holding it. (eg problems re miniturisation of circuits) There does seem to be good scientific (mathematical,metaphysical?) evidence that classical logic is prolific at large scales. This would explain why classical logic worked very well for scientists from newton to the 20th century, but thereafter exploration of the small scale demonstrated that it wasn't enough.

It may be that QM modelling of information matter is radically different to QM modelling of dead matter ...... and further it may be so scale dependent that modelling is necessarily incomplete because a model is itself information written on to a medium. If the model is even slightly larger than what it is modelling, then the model might necessarily be incomplete even if it models (and uses) QM processing.

The metaphysical implications if this were true, would be that life is not completely understandable using classical logic .....and potentially not understandable completely by modelling at all.

I realise that this does not necessarily follow, since 'information matter' may conceivably be modelled by a Quantum Computer, even if information is discovered to be a new fundamental (like spacetime and energy and charge etc.)

1 Reply

@jeeprs,

Welcome to the age of the Petabyte. The End of Theory: The Data Deluge Makes the Scientific Method Obsolete... All models are wrong.
The End of Theory: The Data Deluge Makes the Scientific Method Obsolete

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DNA and the 'Code of Life'

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