Scientists discover double meaning in genetic code

reply to post by The GUT


Yes TG, very nicely put. I was thinking of attempting such a post until I came across yours and then I was like... ah, never mind, I'm covered...

Another clue from the abstract of the article at the Science magazine site.

But before I mention that, first a bit of background into gene regulation.
This wikipedia page into Transcription Factors is a tough read, but the take home message is that Transcription Factors are proteins known to bind to DNA sequences, so that they can regulate how the DNA sequences elsewhere are used to create proteins.

Here's the picture:

*The lumpy pink things are the Transcription Factors, attaching themselves to the DNA.
*The gene itself is a BIT of DNA that is not part of this process, but off to the left of the picture.

So all of that is the current standard known knowledge.

What does this new research by John Stamatoyannopoulos and his team have to say?
Its says:

We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites.

So this new knowledge is that not only do the Transcription Factors bind to DNA sequences outside the genes (as is already known), but they can also bind to DNA sequences within genes.

Thats it.
No aliens required.

The implications for this discovery appear to be that the places where the Transcription Factors bind will not be able to evolve as fast as the rest of the gene. And that what they find, when they use the phrase "highly conserved".

I love watching certain people kick and scream and drag their feet when presented with information that takes us to the next level of knowledge. Even when it comes from their own religion, science. Oh well, I guess it has alway's been this way.

GMO will be like.
"oh shoot! we F$%^ up BIG Time!"

Keep this in mind, and than think about Monsanto and Gmo...

We are modifying with out any knowledge of the potential side effects, we are modifying DNA when we just discovered this?

Something that could be a major component in the out come...

Come on guys you don't really think the amazing medical and life enhancing possibilities of this discovery will actually be used to help us simple folk do you?

No no, we can all sleep easy knowing that only the super rich and elite can even think to afford such treatment.

reply to post by The GUT


If I may, the gentleman was saying that there is nothing specific to this discovery which would cause the scientific consensus in Theory of Evolution to abandon that theory, and jump ship to Intelligent Design. Your comment suggested that there was. As if to say "Due to this discovery, and because of the language used by the authors of this academic article, it is now intellectually honest to subscribe to Intelligent Design". xDdeadcowX pointed out, correctly, that this is not a logical statement.

Cheers

PS, your threads rule.

pandersway
...Scientists have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease...
...

What do we hear almost every day...?
"...Sometimes a cigar is just a cigar..."
Why do you always need to find subtlety, successive layers and alternate explanations...?
Why can't you be satisfied with the simple truth -?-?- It is - what it - is.
Before you know it, we'll be finding conspiracies under every rock and crawl space.

reply to post by pandersway


GREAT find. Now I'm wondering about the relationship between epigenetic mechanisms and this hidden code.

...many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously

benrl
Keep this in mind, and than think about Monsanto and Gmo...

We are modifying with out any knowledge of the potential side effects, we are modifying DNA when we just discovered this?

Something that could be a major component in the out come...

Exceptional contribution!

We had severely limit knowledge/understanding of DNA when we as a species decided we "knew it all" and "how to make it work for us".

We create crops that are missing half the story, with no idea how the long term effects of ingesting those crops can do to real live DNA over time.

I feel this same way toward nuclear energy. Just because we were given the knowledge of the power to create (DNA) and destroy (nuclear energy) doesn't mean we are capable of utilizing that knowledge in the manner it was designed.

How can a pot tell the potter how to make itself????

We were created/designed (a pot), knowing things does not make us a responsible practitioner of such things (potter).

If only our pride could be removed, so we could see the error of our intellectual vanity, before we destroy ourselves through our vain ignorance by claiming to "know it all".

God Bless,

are people still believing Evolution is a process of mutations?

this is intelligent design

The GUT


Is this true?! Would we now have to embrace intelligent design if we're intellectually honest?

this. plus wow. just wow

dark energy = universal intellegence/consiousness

dark matter = use of this energy pulling itself together.

but i may be crazey

reply to post by The GUT

Well, there is somewhat of an oxymoron here, but it resides in the paradox of the linked article as I'll explain in a minute. That is, when 'oxymoron' is used correctly, which you didn't.

Design would always denote intelligence, so that's not an oxymoron even by your misusage. "Intellectual honesty" is a well-recognized phrase that has a decided meaning. Thusly, I hesitate to explain myself to someone with so little grasp of language and inference.

I'll give it a shot, however, because I feel sorry for you.

Well thanks The Gut, i really appreciate you dumbing it down for idiots like me. Could you do me a favor and be more condescending in your future posts? I concede that i used the term oxymoron incorrectly and what i meant was contradiction. This does not change the fact that there is nothing intellectually honest about inserting intelligent design, with zero supporting evidence, as an explanation for finding a second layer of data in a strand of DNA

The University of Washington--UoW being an academic institution--has chosen words such as, "meaning," "code," "write," and "instructions' as descriptors in the linked article.

Those are suggestive and heavy-duty words. You shouldn't need as much of a lesson on their impact as you seem to on the definition of oxymoron---though I could be wrong on that. Read 'em again if you're still lost. It'll hit ya.

Is UW now a prophet who's words are the words of God or are those words owned by religion? You said yourself they are just a academic institution, so i fail to see where you are finding a connection with religion.

Philosophically--and with Occam's in mind--I would further proffer that the idea that this particular and most spectacular of creative forces--DNA--stems from something less than "consciousness" is negated in that we don't even have--at least as far as the University of Washington is concerned--words that don't imply design when describing the theorem. Design, as you'll remember from above, suggests intelligence.

This is not a philosophical subject. If you wanna play Occam's Razor then the simplest explanation is that there two kinds of information instead of one. Period. Making the leap an omnipotent God is nowhere near simple. There is zero supporting evidence for this God you trying to claim designed DNA and there is zero evidence to support DNA being designed in the first place. I get that you may accept this kind of stuff on faith, but you don't get to present your faith as fact.

You are seeing a connection where there is none. You are viewing the subject and the article with God colored glasses. When you approach a subject with a preconceived notion, you are going to see what you want to see, instead of the truth.

Let the scientist handle the science. You never know, one day there may be some verifiable evidence for your God, but it wont be found in a church, it will be found in a lab.

DC

reply to post by The GUT


I have to agree. Although I don't believe in the concept of a creator pushed by religious dogma or spiritualists, that does not mean that someone, somewhere, from this galaxy, universe or the next could not have created us.

That being said, I don't think intelligent design has anything to do with this.

Son of Will
If I may, the gentleman was saying that there is nothing specific to this discovery which would cause the scientific consensus in Theory of Evolution to abandon that theory, and jump ship to Intelligent Design. Your comment suggested that there was. As if to say "Due to this discovery, and because of the language used by the authors of this academic article, it is now intellectually honest to subscribe to Intelligent Design". xDdeadcowX pointed out, correctly, that this is not a logical statement.

I do understand what you are saying, Son of Will, and I admire the nobility of your defense, sir.

Having said that, I saw an opportunity here and admit to a tad of opportunism mixed with some theatrics ha.

I do believe the points made in my post are worthy of contemplation. Those points are certainly not new, but with each slice of knowledge showing ever more complexity and…well…sheesh, what increasingly looks like design (and just about has to be described in those terms) I decided to fish out my poetic license and offer some food for thought.

Cheers

PS, your threads rule.

I sincerely thank you for saying so. That was very nice to hear today.

alfa1

Reading through the postings so far, there seem to be an awfully large number of people ready to throw out everything we know so far on the topic of DNA... and all based on one single press release.

Because thats all this is.
One single press release from the university, advertising their publication in Science.

Details are thin. But what it appears to be saying is that :
- most everything we know so far *stays the same*
- some codons also "appear to stabilise certain beneficial features of proteins and how they are made".


The idea that DNA sequences not only code for proteins, but also code for gene control is not news. This has been known for decades. What the paper appears to be saying (based on the press release) is that some elements within the introns can also function as control data.

I'd like to see more detail than a press release though.

All the researcher are like that - they've been like that since the 1960's if not further. Even back in the 1980's, one woman researcher commented that "everyone likes to thing that they have found the last piece in the puzzle and that the search is complete". Then someone else unlocks another door, and it's another gold rush.

The more work that is done on genetic research, the closer a cell seems to behave like a computer system:

We have cell membranes = network firewalls, security rings

Nucleus = operating system kernel

Genes/Chromosomes = functions/dynamic linked libraries

It is known that the nucleus actually caches those genes that are in active use. In that way it reduces the chances that a gene will be damaged during extraction.

Cell receptors = TCP/IP networking sockets

Most computers have an "instruction set" that could a variety of things: write out data, read in data, execute another function, halt execution, perform parallel processing operations like

Cells can self destruct using a process known as apoptosis.

DNA would seem to be like an instruction set that can write data (the coding for amino acids), but it would also have parallel processing instructions that would activate and stop genes. Those could simply be particular combinations of amino acids. It's known that there is always one codon that encodes as a a "END" instruction.

Depending on the way you look at it, DNA could be a form of microcode, which allows large instructions to be made.

Interesting. It seems living things (or at least more evolved ones) bring along an interpretive layer able to actively rewrite its own code. Execution of what's in DNA may not be as fixed as it seems. This also means that the concepts of Lamarckian evolution might need to be revisited with more scrutiny. At least now there are tools to look at it better, and who knows - some aspects may no longer be considered junk science if reviewed with newer tools and better understanding of some of the underlying biological processes.

I wonder if after we understand it a little better, if the same approach could be modeled or copied in man-made software?

reply to post by pandersway

To me this is news in which mainstream science admits were wrong about DNA and say they don't understand it yet.

Do you think Information ( codes) in DNA could be more than just 2 codes imposed over each other (and it could be connected to all atoms).
The admission of ignorance points to what is not known and that what we have been told of DNA is just theory.

This is very exciting! Wheels within wheels, to use a biblical reference. DNA is even more complicated than anyone discovered, so far!

OrphanApology
reply to post by pandersway

 

AKA as the "double helix of meaning".

The more you know, the less you'll understand.

Thanks for posting.

Well, more like the quadruple helix, I think! The double helix structure was already well known. But it certainly is interesting. More like the DNA containing even more complexity than we thought. But then again, a language within a language is still just a language. There is nothing really revolutionary in this if you think about it. Simply yet another layer.

Agent008
Come on guys you don't really think the amazing medical and life enhancing possibilities of this discovery will actually be used to help us simple folk do you?

No no, we can all sleep easy knowing that only the super rich and elite can even think to afford such treatment.

Yup. As it always has been. Until the revolution comes along or something.

reply to post by xDeadcowx

There is zero supporting evidence for this God you trying to claim designed DNA and there is zero evidence to support DNA being designed in the first place.

Yeah Gut, don't you know this in depth DNA just went POOF out of nowhere? Everyone knows that something intelligent didn't make intelligent beings.....DUH....

/sarcasm

You will one day understand that God did make all life on Earth...Sorry if that day isn't today and I am not here to sway you that way...

God bless