Scientists discover double meaning in genetic code

[Kryten]

It must always be kept in mind that DNA fundamentally isn't a code or a language, it's an actual molecule.

[Technical Ben]

It must always be kept in mind that DNA fundamentally isn't a code or a language, it's an actual molecule.

Again. Go out and check the processes involved. Your stating "It must always be kept in mind that an HDD fundamentally isn't a code or a language, it's an actual magnetic force." Yes, because DNA is not a code, it contains the code. Just as a HDD is just magnets. A clock work Turing machine is just cogs. A usb stick is just silicone. A DVD just tin foil and oxidisation. But none of those things are "just molecules", but actual functional objects.

DNA is a molecule. The processes applied on it are of copying, translation, transcription, recombination, error checking, etc, etc, etc. These are not "chemical" functions, though they are chemical processes, they are mechanical processes.

Just as space flight is via chemical processes, we do not call a solid rocket booster "just a molecule". Do we?

Calling DNA just a molecule, is like calling a Computer, with a HDD, DVD drive, RAM and CPU as "just a silicon reaction with magnetic attraction". That's it's materials, not it's observed mechanical function (or just "observed action", if removing all possible accidental "intent" from our observations). It's correct to call it that, but incorrect to argue it thus holds no "code", just as it's wrong to argue my computer holds no "code". Defining c# on my HDD may be difficult, but it's certainly a scientific fact.

First prove to me my OS does not exist, and this forums software is not coded, then I could understand why people are attempting to suggest the same functions applied to DNA + cellular machinery also does not exist as a "code" within such a system.

Edited July 26, 2015 by Technical Ben

[shynung]

Molecules. It's more of a large string of organic molecules arranged in such a structure that, when processed by a cellular transcryption system, produces a precise and consistent type of protein. Then again, so are ink-on-paper letters; a collection of paper molecules and ink molecules arranged in such a way that, when read by a human with compatible knowledge, conveys a particular message or idea.

Calling DNA a 'code' or 'language' is just an effort to make it convenient to understand how they work. Just as it is convenient to regard a single animal as an independent entity rather than a collection of cells and DNA when studying their social behaviour.

Edited July 26, 2015 by shynung

[Aanker]

... Yeah but what's the point of diminishing either perspective? Looking at DNA as a molecule is useful in many specialized fields (especially when trying to detect DNA) but for other purposes it is more convenient to regard it as a code (especially when planning transfections, for instance).

[shynung]

... Yeah but what's the point of diminishing either perspective? Looking at DNA as a molecule is useful in many specialized fields (especially when trying to detect DNA) but for other purposes it is more convenient to regard it as a code (especially when planning transfections, for instance).

You are right. One perspective is useful for some purposes, other perspectives for others. Neither is more correct than the other.

[Technical Ben]

That's great then!

Who said it cannot be a molecule with both a chemical reaction and contain a code? Is a HDD not also a bit of magnetic metal and contains a code?

Then again, so are ink-on-paper letters; a collection of paper molecules and ink molecules arranged in such a way that, when read by a human with compatible knowledge, conveys a particular message or idea.

Which is an amazing system. Of any construction, it's always more than just "chemistry", right? A book, in context of pages and words, is more than just "chemistry of ink and wood". Why? Ink and wood have no specific physical property to arrange as they do. They require construction to be in that specific arrangement. I would have thought the construction can be any means, and is not restrained by or to chemistry (we can have a Kindle, a TV or a book showing words and being used in context).

Is this true of the code in DNA, the transcription mechanisms applied to it and at work in a cell?

The statements and observations I've seen in biology papers and other more laymen explanations, has been that chemical bonds in DNA have no preference on the ordering of the nucleotides. Yes, all physical iterations have an effect on all things, but in this case not to a (significant) extent to effect things. For example even the Codon table, I've seen described as also being free from chemical influence, in that it can also be arbitrarily chosen (we can theoretically assign any tRNA type to produce and any nucleotide->RNA->tRNA->Amino Acid ordering we wish, thus so can nature).

So is it a coded system, a mechanical system, or a chemical system?

Edited July 26, 2015 by Technical Ben

[Kryten]

The analogy doesn't work too well, because the information in a book is entirely separate from the book itself, whereas DNA is an inherent part of the system it's feeding information into. Even the protein-coding areas will produce different results in different organisms, as the genetic code proper (i.e. the codons) isn't entirely consistent.

[shynung]

That's the main difference between books and DNA; a typical book does not contain enough information and instructions that, when followed properly, results in more books. DNA becomes an inherent part to the system it fed information into because the system's only purpose is to replicate and propagate the DNA; rather difficult to copy a book by hand if you're not looking at it a few times, no?

Also, unlike someone copying a book by hand, DNA replication is inherent within the information. It's as if the 'book' (DNA) have a line at the end that says, 'Copy this book as much as you can, and give it to everyone'.

Edited July 26, 2015 by shynung

[Technical Ben]

The analogy doesn't work too well, because the information in a book is entirely separate from the book itself, whereas DNA is an inherent part of the system it's feeding information into. Even the protein-coding areas will produce different results in different organisms, as the genetic code proper (i.e. the codons) isn't entirely consistent.

That statement is observed, tested and scientifically shown to be false. If the codon table produces different results, it proves it's part of a code, not part of a reaction. That's what a code under a different translation mechanism does, it gives different results (or junk in, junk out). Thus showing it's not bound by chemical results that are required to give the same result. If it was bound by chemical reactions, it would give the same result in all animals, as chemical reactions always give out the same substances each time.

Language is flexible, it can be English, French, Spanish etc. Chemicals always give the same result. Ink in a book is not a chemical reaction, it's data for us to use. Do we see the ordering of the nucleotides in DNA to be chemically restricted, or to be chemically free?

For example, tRNA, the codon table and the arrangement of nucleotides are all able to hold arbitrary information. It's true that as with everything in existence they are bound by the laws of physics. They are effected by chemical reactions. But so is my HDD on my pc. So is a DVD. So is a car and a computer. Does it effect the data held within them?

shynung, a book can be a library. A book or library can easily contain the information required to produce more books mechanically. A DVD can. There is enough of a separation, and many scientific papers on it, of the data and mechanical properties in DNA, for me to confidently state it is not bound by them as to it's ordering of it's nucleotides.

That ordering does effect it's larger structure, just as it can do so in a book, HDD or DVD. But the structure of the data, is again not linked or a limiting factor to the information in that data. For example, I have to be limited to a page in a book, or a sector on a HDD/DVD, but can put any arbitrary data within that. So science can currently see there is structure (physical limits in DNA), but there is also freedom to it's ordering (it can code for any protein, via any codon table of choice).

If we can (and we can), choose any arbitrary codon table, and any arbitrary dna sequence, to produce and arbitrary protein, how can we state it is chemically or physically constrained?

TLDR version, the DNA it's transcription and translation, it's codon table and the tRNA each contain "free" information, that can be assigned any other chemical bond. Thus they are not chemically restricted (eg any nucleotide order for any nucleotide substitution to any amino acid).

Edited July 26, 2015 by Technical Ben

[KerikBalm]

I don't know why "technical" ben keeps insisting on some "mechanical" process over "chemical", as with the "what is life thread"....

There is no need to try and reduce what it does/is into such a narrow definition. Someone who wants to be technical should not try to oversimplify things.

DNA is deoxy-ribonucleic acid. It is not a code.

You can encode stuff with a sequence of DNA, but DNA itself is a molecule with specific chemical and structural properties.

I can use a set of building blocks to spell letters, or to build things. That doesn't make building blocks a code.

DNA is a structure

DNA can be a template

DNA can encode things.

Not all DNA is there for structural purposes. Not all DNA is there as a template. Not all DNA encodes things.

Some sections of DNA can do more than 1 of those 3 functions.

- - - Updated - - -

That statement is observed, tested and scientifically shown to be false.

That above statement is 100% pure unadulterated garbage.

The rest of what follows doesn't make much sense either, but not worth responding to anyway as its just a failure of "ex falso quodlibet"

Edited July 27, 2015 by KerikBalm

[KSK]

So is it a coded system, a mechanical system, or a chemical system?

All three. A code has to be encoded on or in something.

To use your hard drive example, information is encoded as magnetic domains on the a drive platter and is written to or read from that platter by the electromechanical systems in the rest of the drive. Trying to describe a hard drive as either a coded system, or a magnetic system or an electromechanical system, doesn't work - it's all three together. The binary code stored on a disk platter isn't much good without the rest of the disk drive to read it and conversely, a blank hard disk isn't going to run your computer.

Likewise, DNA is a polymer with certain chemical properties that enable it to encode information and certain mechanical properties that determine how that information can be accessed (DNA needs to be unwound before it can be transcribed) And much like my hard drive example, the information encoded in DNA is meaningless without a larger system to read it and act upon it.

[Technical Ben]

Thanks KSK. A nice informative and polite reply.

So DNA has many properties and is observed to contain a code that cellular mechanisms can use.

Why would anyone wish to deny that?

[WinkAllKerb'']

you can either keep on reading thing like an individual that live 0 to 130 years and never understand the mutligenarationalintra&inter species you miss, or read thing like someone who live 0 3000 years (random number as exemple).

if i was an individual molecule like h20 and want to write something in the rock i ll probably ask other molecule to help me doing so upon a few generations ... even if it took a long time and most of us end probably recombined when the work is done ...

(merge with previous picture tks) <= this is pretty much a metaphor for multigenerational/intra/inter layers of reading as exemple for species adjustement // there environnement @ long time scale wich do not exclude at all mitosis from one generation to the direct next one ...

(also notice that being so much entitled in the 0 130 approach of thing is just boring to me and tend to make me giggles a lot, especially when so called scientist are stuck in this selfish time egotist time loop ... just sayin')

Edit 1: code is a language someone is unable to interpret or read due to a restricitive & limitative approach at some point. (Like for exemple time & "n" dimensionnal approach related)

via Imgflip Meme Maker

*shrug* i kinda feel hungry and thirsty right now *nevermind* i'll probably find something that fit what i need with the next re-generation; )

Edit 3:

via Imgflip Meme Maker

notice that it cannot be related to the fact that we don't speak at the same speed(s) and do not use the same "layers" and """translocated "n" dimensionnal""" lifespans & process ...

that's also why abstracting thoose links while considering DNA tend to now be 101% silly to make further progress ... wich is equal to: if you want to understand DNA better link it to smaller and bigger thing @ different scale related (size/time/other languages >chem,phy,neuro,elec,magnet,etc.<) etc. etc. etc.

=> https://en.wikipedia.org/wiki/Feedback <=

Edited July 27, 2015 by WinkAllKerb''
...

[Darnok]

There is no need to try and reduce what it does/is into such a narrow definition. Someone who wants to be technical should not try to oversimplify things.

Actually nature likes simple solutions, science should do same thing... https://en.wikipedia.org/wiki/Occam%27s_razor

I can use a set of building blocks to spell letters, or to build things. That doesn't make building blocks a code.

Hmm https://en.wikipedia.org/wiki/Code_%28disambiguation%29 see "Building code, set of rules that specify the minimum standards for constructed objects" in very general way DNA is building code for your cells? Your building blocks are cells and DNA is plan how to use them?

Maybe you should write your definition of code

[KerikBalm]

Thanks KSK. A nice informative and polite reply.

So DNA has many properties and is observed to contain a code that cellular mechanisms can use.

Why would anyone wish to deny that?

Seems fine with me. It definitely contains code, but there is so much more going on there than just a code.

- - - Updated - - -

Actually nature likes simple solutions, science should do same thing... https://en.wikipedia.org/wiki/Occam%27s_razor

#1) That isn't Nature, that is human philosophy.

#2) That refers to taking the simplest *explanation* that fits the *observations*

It doesn't apply to making definitions, and it certainly isn't relevant if it doesn't fit all the observations

Hmm https://en.wikipedia.org/wiki/Code_%28disambiguation%29 see "Building code, set of rules that specify the minimum standards for constructed objects" in very general way DNA is building code for your cells? Your building blocks are cells and DNA is plan how to use them?

Maybe you should write your definition of code

Maybe you shoul understand the definition you quoted.

"set of rules"

DNA is not a set of rules. Rules are abstract non-physical things.

DNA is a physical thing.

The base pairing interactions allow it to form physical structures, and act as a physical template.

DNA is basically a structure and a template for RNA.

Some of that RNA contains a code for protein, some doesn't.

[KSK]

Thanks KSK. A nice informative and polite reply.

So DNA has many properties and is observed to contain a code that cellular mechanisms can use.

Thanks. Interestingly, your earlier comment: "we can theoretically assign any tRNA type to produce and any nucleotide->RNA->tRNA->Amino Acid ordering we wish, thus so can nature." was pretty accurate too - at least according to my (limited) understanding.

Nature is a bit constrained due to 'backwards compatibility' problems - a mutant tRNA that starts adding the wrong amino acid into a peptide sequence is highly likely to be lethal because any cell with that mutation is highly likely to be churning out a large percentage of nonsense proteins that don't fold correctly and so don't have the expected function. Not all of them mind - you can make so-called conservative substitutions into a protein structure, where small changes to the primary structure (amino acid sequence) don't result in a malformed protein.

However, because the genetic code is degenerate (64 possible codons encoding approximately 20 amino acids), there is room for some clever tricks. One very neat example is to engineer a cell line with a custom tRNA such that one of the redundant codons is re-mapped to phosphoserine. This isn't (I don't think) a naturally occurring amino acid but culture your cell in a phosphoserine containing medium and it'll quite happily absorb it as a nutrient. You can then use your cell line as a 'factory' for churning out proteins which are phosphorylated at a particular site.

This is a big deal because an awful lot of cell signalling pathways rely on protein phosphorylation to work, so having a research tool that can make them to order is huge.

[KerikBalm]

You could change the tRNA anticodon, if you also then go change every codon in the mRNA/DNA template for mRNA so that the same amino acid is specified.

This has actually been done in a bacteria through a comlicated series of mutation.

At one point I wanted to do it in a mitochondria by just artificially synthesizing the whole genome... but getting functional DNA of any sort into mitochondria is quite hard.

You would also need to preserve the initiation and stop codons, or get into even more complicated changes to the release factors and translation initiation

[KSK]

Actually nature likes simple solutions, science should do same thing... *snip*

Not really, or at least not in biology. Evolution is blind - it proceeds step by step, each step building on the one before. However, at each step, nature is kind of stuck with what it has at that moment - it can't (or is extremely unlikely to be able to) do a 'roll back' to a previous step, even if being able to start from that previous step would make make more sense to an outside observer.

Granted, evolution can produce some beautifully optimised structures but it can also (especially in cell biology) produce some truly Rube Goldberg designs where parts have been swapped around, repurposed on the fly, or used for a whole bunch of disparate functions.

Check out GAPDH as an example. Originally identified as a metabolic enzyme, we've since found out that cells also use it for a whole bunch of other purposes.

[WinkAllKerb'']

https://en.wikipedia.org/wiki/Compact_disc

&

https://en.wikipedia.org/wiki/Error_detection_and_correction (eventually this also: https://en.wikipedia.org/wiki/Hash_function)

&

https://en.wikipedia.org/wiki/Burst_error-correcting_code

more or less the same process applied to DNA // time // chemical & non com. process imho