Scientists discover double meaning in genetic code

[Bill Phil]

*sigh* this is the problem with pop-sci reports

There is no second code here.

There's some proteins that bind specific DNA sequences.

To specify a given amino acid, you have multiple choices of DNA sequence.

In some cases, those choices are selected to create a sequence a protein will bind to.

DNA is not just a code, it is a physical structure, and things physically interact with it.

This isn't a 2nd code, this is a structural constraint for transcripton factor binding.

This forum needs an ignore feature, or a down vote feature.... I don't know how much more of Darnok's pseudo-science drivel I can take in the science forums.

Aren't you forgetting about introns? They don't code for proteins, and are "cut out" before mRNA codes for proteins. I don't think we know what they do just yet.

[Technical Ben]

Hey, if the article is speculation and hyperbole, why not check the data ourselves?

Talk by the scientist on his paper, with questions and admissions on what the limits of knowledge are, but also on how accurate the observations are. https://youtu.be/SE7AesCVkp0

[smjjames]

This whole hidden code/double meaning sounds conspiracy-theoristy, maybe it's just the wording of the title. Honestly though, I would like actual evidence and a better explaination of the whole thing.

[LordFerret]

This whole hidden code/double meaning sounds conspiracy-theoristy, maybe it's just the wording of the title. Honestly though, I would like actual evidence and a better explaination of the whole thing.

For that, you'll need to read the published papers / scholarly articles on it and all related research. I've spent the better part of the morning here doing just that. Interesting stuff, just the tip of one of the icebergs out there related.

[vger]

Yay, let's ruin a perfectly fine thread by trolling with nutter antivax propaganda!

This barely has anything to do with antivaxxing. Only when it involves DNA vaccines, which right now are only a tiny percentage of all vaccines. Antivaxxers oppose ALL vaccines, not just DNA, and think there is some vast conspiracy to poison civilization. Though unfortunately for science, this confirms one of the things the paranoid right has been concerned about for a long time - that DNA "hacking" is a hundred times more complicated than we think it is.

Frankly, I'm more interested in the GMO issue. GMO company's PR problems probably just increased 10-fold.

[shynung]

Aren't you forgetting about introns? They don't code for proteins, and are "cut out" before mRNA codes for proteins. I don't think we know what they do just yet.

They may be 'passenger' gene sequences. That is, they just hitched a ride (get absorbed) by the ancestors several million (or billion) years ago, but isn't of much use to the ancestor creatures. Those who decode these introns may get some sort of handicap, so the ones evolving countermeasures (enzymes that 'cut' the introns out) gets an evolutionary boost. Though, since DNA duplication is all-or-nothing, the introns get copied along with the rest (thankfully, the 'editor' enzyme gene gets copied too).

The other possibility is that the introns are genes injected by retrovirus, a kind of virus that slips its own DNA/RNA sequence into the host's DNA. This infection, once initiated, stays indefinitely; that's why HIV is hard to treat, as it is a retrovirus. In this sense, 'editor' enzymes that cut out introns may be the cell's defense mechanism against unwanted sequences; even though it can't erase it, it won't be very harmful if it isn't actually coded into proteins.

[Technical Ben]

Why argue over it, and not actually look at the evidence first before we make any comments on the facts?

Presentation of the actual data.

[KerikBalm]

No, as far as I know, there are multiple overlapping codes within DNA. So, depending on the description, we can say "there are double codes".

Within a given reading frame, there is only one code.

CTG is a code for an amino acid.

There may be other features, like CTGACG being a binding site for a protein...

You can look in another reading frame, and see TGA instead of CTG.ACG TGA... being a stop codon, would truncate the protein.

That there are alternate reading frames is multiple decades old... otherwise frameshift mutations would be unheard of. Genes being encoded on both strands with some overlap is also decades old.

The CTG code doesn't change.

The nucleotide-amino acid code doesn't change

Due to either it's nature or it's necessity, DNA has in built compression/redundancy via this method.

Its not much of compression, the percent of overlapping coding sequences is quite small.

And its not redundancy either.

I would have thought a proof on the structural requirements for the ordering of DNA would earn anyone, you including, a Nobel Prize. The entire consensus and observations currently attribute no preference for the DNA ordering due to atomic or mechanical forces. Only the mechanisms of reading/transcribing etc. The example of a double code, is an example of ordering, not of mechanical function and not of physical constrains.

More incoherent BS.

DNA is not 1's and 0's... it is a physical thing, with physical interactions. Many base pairs are just there for proteins to bind to. Many aren't there as a code, but as a template for non-coding RNA....

etc

PS, the article states on the "new code" discovered, "One describes how proteins are made, and the other instructs the cell on how genes are controlled."

So it appears it's talking about Gene expression, and not just overlapping encoding sites.

I don't give 2 ****s what a laymans article says. Its not a code... its inclusion of binding sites within the coding sequence.

Still, points stand. Gene expression is an observed fact. If it means we need to write in new details and change our understanding, do we choose to be dogmatic, or choose the evidence? I choose the evidence.

You choose to make statements on stuff you clearly have a rudimentary understanding of.

"gene expression is an observed fact".... uhh... ok... yes, genes are expressed... very technical language there...

What it shows, and what we've known for decades (google codon optimization), is that chosing different codons can get you the same protein, but expressed at different levels.

That is nothing new. This is just describing 1 mechanism whereby different codons may have different protein expression levels.

Aren't you forgetting about introns? They don't code for proteins, and are "cut out" before mRNA codes for proteins. I don't think we know what they do just yet.

I'm not forgetting them at all... they aren't coding.

They are often physical binding sites for proteins, contain enhancer elements, or do contain coding sequences - look at alternative splicing....

Alternative splicing is more like a compression algorithm than what was mentiond above...

Suppose you want two proteins, that share many of the same domains, but have some differences... have the different parts as part of the same genes, and alternately include them as exons, or exclude them as introns.

There are many little caveats... but this is nothing revolutionary.... ooooh some binding sites within the coding regions... oooh... like we haven't known those occur for years...

oh but now its transcription factors that bind, and you've got a bit of a more nuanced description of codon bias...

OMG, that totally justifies a logical leap to say GMOs and vaccines are bad...

[Technical Ben]

Wow, interesting way to respond there. They can overlap and be internally combined with separate reference frames (with internal ones, it's hard to still state these as separate here, but I'll go with your language and technical terms if needed).

Yes, it's decades old information. The video talks about new data and what this shows, and what is yet left open to learn. New data is new data. No need to shoot it down just because some papers/websites like to make it sound interesting.

The "new" bit was generally about how much is left active and how much is turned off and how much is left without markers on cells that reach maturity (from the obvious starting point of embryonic stem cells). They looked in detail at this second code, the epigenetic, it's what they research.

My understanding is rudimentary, and so is my language skills of something that requires specialist knowledge. Sorry, I did mean "epigenetics effect on gene expression is observed", I missed the first bit out. Did you not infer that from your understanding anyhow? Why not correct me instead of having constant jibes at my silly forum name? Do you see me calling you names for your spelling mistakes? No. I can still read your posts quite well, and be polite about it. We need not devolve into arguments on little human mistakes.

So I'm rudimentary, some help would be appreciated. Explain what is meant by "is that chosing different codons can get you the same protein, but expressed at different levels." Levels of what? What is a "level"? Of reading frames? I know the codon table allows for both error correction/redundancy and for alternate reference frames (the level of redundancy allows "sentences" to have some overlap. Really clever feature. ).

(Who on earth is making this vaccine claim? The comment was on impact, change and learning, not on "panic", was it?)

Edited July 19, 2015 by Technical Ben

[KerikBalm]

level = amount as I was using it

I am not shooting down the work. I am shooting down the hype and misinterpretation of it.

The vaccine claim is Darnok

They are called alternate open reading frames, and they are not relevant to this work.

What this showed was that the proportion of accessible DNA with binding sites for transcription factors was conserved to drive tissue specific expression.

None of this invalidates previous assumptions, or means previous stuff behaves unpredictably in light of this

[Technical Ben]

Ok. "Amount" makes more sense. Thanks.

The article was basic, for those without the specialist information. The video (which presumably the paper/website has not the time nor knowledge to understand), shows the real data and information. The paper/website could only go with the basics of the foundation of their study, epigenetics. Sadly, the title and body was wrong, it's not "new proof of [epigenetics]" but just "new data on epigenetics".

Yep, silly newspaper or website there. Still amazing work on the genetic code.

Alternate reading frames would be included in all genetic work I guess, as it's going to effect nearly all data. But yes, it's not the topic of the study they did, though it does come up (in reference to the locations and spread of the regulatory sites and how they are embedded in the DNA and how they effect and direct the data they need to collect).

Finally,

More incoherent BS.

DNA is not 1's and 0's... it is a physical thing, with physical interactions. Many base pairs are just there for proteins to bind to. Many aren't there as a code, but as a template for non-coding RNA....

etc

By it's nature and necessity, DNA must have no preference to it's base ordering. Any, absolutely any data contrary to this is an earth shattering discovery. A proof in contrary to this, is the flexibility of the codon table and the tRNA. Which means (AFAIK) any ordering can be chosen for any "code" without any structural limit. How and if that effects the amount of non-coding DNA with different codon tables, I do not know. Non coding though areas though, would still be required to be mechanically inconsequential.

Edited July 19, 2015 by Technical Ben

[KerikBalm]

Its well known that GC content is relevant.....

Thats why there are organisms with very high GC content, and organisms with very low GC content.

Your assumption "By it's nature and necessity, DNA must have no preference to it's base ordering." is flat out wrong, and its not earth shattering.

Furthermore, Since a lot of DNA is non-coding (in Eukaryotes), the tRNA decoding system isn't really relevant.

The DNA sequence for centromeres and telomeres is for structural concerns.

DNA sequence for a lot of RNAs is just a template for the RNA. The RNA sequence is often there to make specific structures through base pairings.

And there is even this:

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

Hopefully you can read it and understand it well enough to get my point on that one.

[KSK]

Going to need to read the original work - that layman's summary was next to useless. For openers: "For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made." is blatantly incorrect.

Also, check out the date on the linked article. This isn't exactly new and I don't recall hearing about it anywhere else despite working at a university with a lot of bright people whom I'd expect to be very excited about it.

I'm sure one of the actual biologists here will correct me but it sounds like the article has blown these results out of proportion.

Edited July 20, 2015 by KSK

[PB666]

Its well known that GC content is relevant.....

Thats why there are organisms with very high GC content, and organisms with very low GC content.

Your assumption "By it's nature and necessity, DNA must have no preference to it's base ordering." is flat out wrong, and its not earth shattering.

Furthermore, Since a lot of DNA is non-coding (in Eukaryotes), the tRNA decoding system isn't really relevant.

The DNA sequence for centromeres and telomeres is for structural concerns.

DNA sequence for a lot of RNAs is just a template for the RNA. The RNA sequence is often there to make specific structures through base pairings.

And there is even this:

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

Hopefully you can read it and understand it well enough to get my point on that one.

GC content is important if you are a microbe living in the thermal vent on the ocean floor versus a krill that lives its life in the arctic ocean.

GC content determines the melting point of DNA for a given length. When you do PCR its one of the first things you calculate when trying to determine the annealing temperature.

[WinkAllKerb'']

how do species adapt to there environnement it they not "digest" and/or "integer" there environnement(s) DNA/(non DNA) at some point or another little small part per little small part ... ? .... yeah yeah it might be by "nature" a long and slow "by design" assimilation process probably almost unoticable so much it's slow and small part per small part sorted imho

duplicating/sorting/integer environnement dna in your own cell sound like the more logical process ... (insert time scale here + insert amount per periodism here)

(without taking the radiation process into account wich is one // thread kinda slighty more random)

...

...

...

Edited July 20, 2015 by WinkAllKerb''
addendum non dna related wich is a large non neglectable part ... obvious but added just in case ...

[KerikBalm]

GC content is important if you are a microbe living in the thermal vent on the ocean floor versus a krill that lives its life in the arctic ocean.

GC content determines the melting point of DNA for a given length. When you do PCR its one of the first things you calculate when trying to determine the annealing temperature.

Yes, I know... the point is that it is already well known that the sequence of DNA may be selected for on the basis of the physical properties of the DNA.

Btw....

Has *any post* from WinAllKerb made *any* sense to *anyone* on this thread?

It seems to me he is just spamming gibberish.

[KSK]

Yes, I know... the point is that it is already well known that the sequence of DNA may be selected for on the basis of the physical properties of the DNA.

Btw....

Has *any post* from WinAllKerb made *any* sense to *anyone* on this thread?

It seems to me he is just spamming gibberish.

No - and not just on this thread. He (?) has scrawled graffiti over quite a few threads in the Science forum - I haven't bothered to check for his words of wisdom in any other forums.

[Darnok]

Btw....

Has *any post* from WinAllKerb made *any* sense to *anyone* on this thread?

It seems to me he is just spamming gibberish.

Yes they have, but you have to go on level of abstraction even higher than my posts. If you can't force your self to do that use Google it should find you some clues how to interpret his words.

[KerikBalm]

No, I can't force myself to make unfounded logical leaps, or spend the effort to guess what sort of meaning might have been intended from his incoherent ramblings (or your incoherent ramblings), knowing he couldn't be bothered to put the effort into the communication to make it clear.... I won't put the effort into this communication to try and decipher it.

I suspect it is impossible to decipher, and you simply choose to decipher it the way you want, like you seem to do with everything else (such as the topic of this thread, for example)

[shynung]

No - and not just on this thread. He (?) has scrawled graffiti over quite a few threads in the Science forum - I haven't bothered to check for his words of wisdom in any other forums.

I've seen a few. They're usually relatively incoherent strings of words written in a language that resembles English. Usually, they pop up in controversial threads.

[sal_vager]

Anti-scientific post removed, lets try to keep this thread on topic as well please, and not descend into conspiratorial woo.

Thank you.

Edited July 20, 2015 by sal_vager

[Technical Ben]

Last post in this thread. May I suggest anyone thinking DNA is not a code, to go out and learn about DNA, transcription and translation (depending on cell type) and the control mechanisms involved in gene expression. Then ask yourself, does the scientific community and scientific definitions call these things "code" or does it call it something else?

[WinkAllKerb'']

dna is a language not a code exactly and it evolve the same way as languages does mostly ...

[ZetaX]

dna is a language not a code exactly and it evolve the same way as languages does mostly ...

Look up what a code is. DNA (or to be more precise: the genetic code) fits it perfectly.

[shynung]

Let's not forget that words and languages are tools for us to use, not something to be riled up on. So, it doesn't really matter whether we call DNA a 'code' or a 'language'; what matters is that certain sequences designate specific amino acids, which then combine to form proteins/enzymes.

Also, regarding OP, here's the Google search results on the main keyword of OP's article: 'duon codon'. And here's the first link in those results that aren't a blog or popular media site.

Edited July 26, 2015 by shynung