Scientists discover double meaning in genetic code

[Darnok]

http://www.washington.edu/news/2013/12/12/scientists-discover-double-meaning-in-genetic-code/

The discovery of duons has major implications for how scientists and physicians interpret a patient’s genome and will open new doors to the diagnosis and treatment of disease.

“The fact that the genetic code can simultaneously write two kinds of information means that many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously,†said Stamatoyannopoulos.

Interesting what impact it has on GMO and vaccines

[MinimumSky5]

GMO yes, but what impact would it have on vaccines?

[Darnok]

GMO yes, but what impact would it have on vaccines?

http://www.who.int/biologicals/areas/vaccines/dna/en/

Recently, a radically new approach to vaccination has been developed. It involves the direct introduction into appropriate tissues of a plasmid containing the DNA sequence encoding the antigen(s) against which an immune response is sought, and relies on the in situ production of the target antigen.

Many aspects of the immune response generated by DNA vaccines are not understood. However, this has not impeded significant progress towards the use of this type of vaccine in humans, and clinical trials have begun.

This one is just great

[ZetaX]

This one is just great

Stop engaging in some kind of quote-mining. You at least gave the entire sentence, but the way you bolded it is very suggestive and changes the meaning.

Apart from that, what is your point¿ That letting some people die is better than try experimental vaccines¿

[Accelerando]

Stop engaging in some kind of quote-mining. You at least gave the entire sentence, but the way you bolded it is very suggestive and changes the meaning.

Apart from that, what is your point¿ That letting some people die is better than try experimental vaccines¿

It's okay to express your intent to let your kids die and put thousands at risk for want of a vaccine, of course, as long as you qualify yourself with a condescending smiley face :-)

[Darnok]

Stop engaging in some kind of quote-mining. You at least gave the entire sentence, but the way you bolded it is very suggestive and changes the meaning.

Apart from that, what is your point¿ That letting some people die is better than try experimental vaccines¿

Look at OP article it did change meaning of every genetic experiment ever released and used in production on living humans, on animals or any other products we eat or in DNA vaccines.

After those studies you can't say we did understood any DNA modifications or that we predicted any harmful effects, because we didn't!

Companies making any DNA modifications for years had no idea what are long term consequences and by long term consequences I mean few generations ahead, not alzheimer or cancer on people they were study today.

What is even more interesting we can't say we can ever be able to understand DNA engineering, because we can't say today how many different meanings there is encoded in DNA.

Maybe there are 3 or 4 or more ways to decode DNA, so any modifications puts people at risk, I doubt it anyone aware of danger and harmful effects, that may occur in future generations, would ever take that risk.

Edited July 19, 2015 by Darnok

[WinkAllKerb'']

exactly

(infinetesimal random addition+ infinitesimal random addition x a numerous lot not even countable time through generation and environnement)^more or less infinite time= ...

this is the equation some are playing with ... and actually tend to act like considering thoose infeintesimal addition suppression are neglectable on the long run reproduce and evolve process overall ... tricky tricky 0 130 approach imho ...

Edited July 19, 2015 by WinkAllKerb''

[lajoswinkler]

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

[ZetaX]

In regard to those GMO claims, let me just drop this: http://www.slate.com/articles/health_and_science/science/2015/07/are_gmos_safe_yes_the_case_against_them_is_full_of_fraud_lies_and_errors.html?wpsrc=sh_all_mob_tw_top

Look at OP article it did change meaning of every genetic experiment ever released and used in production on living humans, on animals or any other products we eat or in DNA vaccines.

No, that's what you interpret into it. Anyway, other doing bad thing does not allow you to do the same.

What is even more interesting we can't say we can ever be able to understand DNA engineering, because we can't say today how many different meanings there is encoded in DNA.

Maybe there are 3 or 4 or more ways to decode DNA, so any modifications puts people at risk, I doubt it anyone aware of danger and harmful effects, that may occur in future generations, would ever take that risk.

While vaccines might have some unintended effects, those in our food are not relevant. They are simply digested.

@WinkAllKerb: I have no idea what you actually want to convey.

@lajoswinkler: well, it's the thread starter that is doing this...

[WinkAllKerb'']

f1 f2 hybridation clone = ? ... i need a seed, an asteroid redirect mission and a few G to bring as much environnemental component as i can into the trip ... *bored*

a yeah now aside genetic crossing matter let's talk a little about energetic cost solution ... *B O R E D*

Edited July 19, 2015 by WinkAllKerb''
i think i mean that i m just *bored* ; )

[magnemoe]

Look at OP article it did change meaning of every genetic experiment ever released and used in production on living humans, on animals or any other products we eat or in DNA vaccines.

After those studies you can't say we did understood any DNA modifications or that we predicted any harmful effects, because we didn't!

Companies making any DNA modifications for years had no idea what are long term consequences and by long term consequences I mean few generations ahead, not alzheimer or cancer on people they were study today.

What is even more interesting we can't say we can ever be able to understand DNA engineering, because we can't say today how many different meanings there is encoded in DNA.

Maybe there are 3 or 4 or more ways to decode DNA, so any modifications puts people at risk, I doubt it anyone aware of danger and harmful effects, that may occur in future generations, would ever take that risk.

None has done any GM on humans and its pretty far off. Only thing who has be modified and uses outside of a lab is bacteria and plants both going trough multiple generations of breeding before getting used.

On the other hand we have no control over random mutations.

Only thing this study shows is that genes is complex, its not an nice file like an KSP craft file its an evolved system and they tend to be messy.

[WinkAllKerb'']

if multiplying crossing and backcrossing can't be wrong ... reducing it ; it's another story ... nah really i think some are really dumbselfhish [snip] ... just cut there head off and that's all ...

Edited July 19, 2015 by Vanamonde

[Hcube]

@lajoswinkler: well, it's the thread starter that is doing this...

after all he is the one that denied the existence of the restricted relativity in a previous thread... some "rutter antivaccine propaganda" was to be expected !

On topic :

@Darnok : this is (very) old news and changes nothing to the classic genetics experiments (cross test...) and the more advanced ones You said that this discovery invalidates every single previous genetics experiment but this is only your interpretation (wich is wrong). for example it was already known that some codons could behave (aka be interpreted and traduced) differently depending on the environment and in the "environment pressure", the fact that some new dimension of data encoding was found doesn't invalidate the rest...

[Darnok]

In regard to those GMO claims, let me just drop this: http://www.slate.com/articles/health_and_science/science/2015/07/are_gmos_safe_yes_the_case_against_them_is_full_of_fraud_lies_and_errors.html?wpsrc=sh_all_mob_tw_top

While vaccines might have some unintended effects, those in our food are not relevant. They are simply digested.

So it is no mater what I eat it won't hurt me, interesting.

No, that's what you interpret into it. Anyway, other doing bad thing does not allow you to do the same.

@lajoswinkler: well, it's the thread starter that is doing this...

I don't get bold part.

DNA vaccine != vaccine... or this is again only my interpretation?

[WinkAllKerb'']

( )

... some "rutter antivaccine propaganda" was to be expected ! ...

()

baaaah .... *shrug* ... current subway spam here (and it's few variations) ¿3 ¿3 ¿3

Edited July 19, 2015 by WinkAllKerb''

[shynung]

So it is no mater what I eat it won't hurt me, interesting.

Vaccines present in food products (e.g. meat from a vaccinated animal) has no effect on humans. They get digested, and are harmless.

A solid chunk of high-purity Beryllium is not harmless if ingested.

Edited July 19, 2015 by shynung
emphasis

[WinkAllKerb'']

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

nahhh seriously ? ...

i need some more explain around the goods exchange "my ass "nati" " law related to milk and https://en.wikipedia.org/wiki/Fermentation ... and biotics

a yeah i remind some eat beef with growing hormone and are good at basketball almost forgot oops ... my bad xDr => TV Show NBA anyone ? a yeah now it's about geopolitcs/sociopolitics/dna process applications from a ant colony pov ... not science at all ...

Edited July 19, 2015 by WinkAllKerb''
*bored*

[ZetaX]

So it is no mater what I eat it won't hurt me, interesting.

Yeah, you are good at quote-mining. Stop putting stuff completely out of context already. Unless you seriously think that "vaccines" is synonymous to "all matter in the universe".

By the way, the same argument applies to DNA/RNA, forgot to also list that.

I don't get bold part.

DNA vaccine != vaccine... or this is again only my interpretation?

I have no idea what your response even has to do with the bold part. My post was talking about you quote-mining and justifiying it with others supposedly quote-mining as well.

[KerikBalm]

*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.

Edited July 19, 2015 by KerikBalm

[PB666]

The short answer to the OP post.

Since the first thorough GWAS of low penetrance diseases such as RA, T1D, GSE ect, it has been realized that the non-HLA genes exhibit QTL qualities but the SNPs (genomic markers) are often far from classic or extended promotor regions. They often lie within the transcription reading frame. The news is not new. Its been known for a long time. In addition there are siRNA found in these genes that either regulate themselves or other genes. So double coding is also known and characterized. There are site in the human genome that are over 500,000 nucleotides were a 350 bp site regulates three genes all from an extended distance.Mutations around this site are known to be associated with QTL variation at the site. Other QTL mutations occur in gene deserts. And last but not least, there are certain sites in the human genome that have a rather disturbed evolution. 6p21 is one of these sites, in Europeans 2 haplotypes are known to have the longest identifyable runs of homozygosity in the human genome, linkage disequilibrium to one of these sites and haplogroup mutations suggest it is 20,000 years old with a rate of recombination 10 fold less or more than the other haplotypes or other parts of the genome. This is particularly odd since the most conserved part of the haplotype represents some of the fastest evolving sites in the human gemome, with 5 genetic loci being the fastest evolving coding sequence loci in the human genome. There is a lot of stuff coded into the DNA that we know is controlling both expression and evolution of the genome itself, and we have known this since the early 70s. The IL2/IL21 locus is another site that has disturbingly slow recombination, and a site on chromosome 5 in Native Americans has also been identified that is half the length of the 6p site that also does not undergo recombination at a normal rate.

Be wary what you read in Science, it does not have a stellar scientific reputation with regard to opinions or retractions, It is better to get information from field specific journals.

With regard to vaccines. Many AD mutations are increases and some are decreased. A fair number of Non-6p21 mutations are in apoptotic machinery, which goes to ways. Either they increase apoptosis of cells (such as beta cells in T1D, or lamina propria cells in GSE) or decrease apoptosis of immune cells such as killer cells or B-cells that cause the disease. If you go about promoting or inhibiting expression you can make disease worse.

[WinkAllKerb'']

yup yup : /

[Technical Ben]

*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.

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". We can easily spot one, and miss the other overlapping code. It could be protein encoding, and easy to spot the one, and miss the second protein encoded over the top, or read in the opposite direction. But AFAIK at least one overlapping encoding area has been observed: https://en.wikipedia.org/wiki/Overlapping_gene

An amazing thing to learn, and a rather rudimentary a concept.

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

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.

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.

Though if I am wrong in my understanding of those systems, I'm happy to hear more on the subject.

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. 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.

Edited July 19, 2015 by Technical Ben

[YNM]

I'm no established biochemist or molecular biologist but AFAIK vaccines are just antigens without the intact, live and sound, invading organism (or virus). Which is needed for IgM (antibody - get over it) to figure and remember it out. Antigens are mostly easy to recreate outside of the body, and this is the preferred method AFAIK. Releasing an antigen-making DNA would be risky if it even doesn't mutate or do something else, for that the DNAs itself are antigens (who says they can't be inside the body cell already ?), not to mention they might not produce the antigens. Also, shipping them with an alive and sound organism (or virus, but virus mostly contains RNA and not DNA...) means you're just making someone truely infected. So, I should say we won't see them, same as you don't see someone learns to drive from start with a standard car and unatended (it's possible but should be a tad riskier).

[AngelLestat]

amazing, is incredible what evolution does with just time.

[WinkAllKerb'']

bah just nTMF ... nTMF ... somehow ... 'sigh' ... https://en.wikipedia.org/wiki/Dual-tone_multi-frequency_signaling