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Reprogrammed bacterium speaks new language of life.

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posted on Oct, 17 2013 @ 02:41 PM
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So I came across this article today and found it extremely interesting.

www.newscientist.com...|NSNS|2012-GLOBAL|life#.UmA1fVDFVv8.

The article starts out to say that they have been able to manipulate and completely change the meaning of the "words of life". When they say the words of life they are referring to codons. Which are a three letter code read by the ribosome , each set of three letters (codons) give specific instructions to the ribosome on which amino acids come next in the chain.

This excerpt kind of lays down the process on how they are ably to change these codons meaning and what its applications imply.



Although there are 64 ways of combining four letters, only 61 codons are used to encode the 20 amino acids found in nature. This means that some of the codons encode the same amino acid – a phenomenon called redundancy. The three combinations left over, UAG, UAA and UGA, act like a full stop or period – telling the ribosome to terminate the process at that point. When this happens, rather than an amino acid getting added to the chain, a release factor binds and triggers the release of the peptide, so that it can be folded and processed into a protein.

A team of synthetic biologists led by Farren Isaacs at Yale University have now fundamentally rewritten these rules. They took Escherichia coli cells and replaced all of their UAG stop codons with UAAs. They also deleted the instructions for making the release factor that usually binds to UAG, rendering UAG meaningless.

Next they set about assigning UAG a new meaning, by designing molecules called tRNAs and accompanying enzymes that would attach an unnatural amino acid – fed to the cell – whenever they spotted this codon. Many such amino acids have been designed, but they can't usually be processed by living organisms and incorporated into their proteins. By reintroducing UAGs at specific locations within genes, the team were able to add unnatural amino acids into proteins at will.

"We now have an organism that has a new code, and we can reliably and efficiently open up the chemical diversity of proteins by introducing a whole new array of amino acids using UAG as the codon," says Isaacs.


The article is very interesting with lots of great info. I'll highlight a few of the tidbits that I think ATS readers would appreciate and that may make a few of you go



"It has great potential for the future to not just replace one here and there, but to replace loads of them and have completely new types of biopolymers made in cells. It's a first step down the road to a new biology," he says.



"[Isaac's team] argue that they can recode living existing genomes quickly and efficiently which can increase biological diversity."


However I think its still to early to jump on the zombie creating bacteria and viruses bandwagon.


What's more, there's little threat of recoded E. coli swapping genes with its natural counterpart, were GROs ever to escape into the wild. Reassigned stop codons would be read as normal stop codons in natural cells, resulting in the premature termination of protein production. Preliminary studies also suggest that GROs cannot grow in the absence of the unnatural amino acid they've been designed to incorporate – adding another level of security.


See its all going to be OK....... Take their word for it. They would never make a mistake and underestimate the complexity of nature and the fact that life will always find away....


So whats your take ATS?

I think that the make some really good points about creating protected batches of penicilin , and being able to make a virus with a UAG sequence unreadable and pretty much stopping it in its tracks. Or creating new medicines and adhesives.

My final conclusion: The can of worms is already open, let see whats at the bottom of the can.




posted on Oct, 17 2013 @ 03:44 PM
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At last, they have created the T-Virus haha.

Next zombies and rampant dogs will take us all!



posted on Oct, 17 2013 @ 04:13 PM
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reply to post by TheLotLizard
 


Well the team that did this research was led by Dr. Isaacs. The Dr. in Resident Evil that ran the Nemesis program for the Umbrella Corp was also named Dr. Isaacs..... No joke


Spelled the same too.

bbs.yale.edu... Our guy.

residentevil.wikia.com... Their guy.

The plot thickens Duh Duh Duh.........
Hows that for synchority lol.
edit on 17-10-2013 by CitizenJack because: Typo



posted on Oct, 17 2013 @ 04:16 PM
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Those who do these things are educated... but are they intelligent?...



posted on Oct, 17 2013 @ 04:34 PM
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reply to post by CitizenJack
 


Thank you for posting.. There was a movie called Blade Runner several years ago that may have been more of a future for mankind than many realize.

Knowledge in these days and times marches on, trying to discover how things work... If we do not do it and get to the bottom of your can of worms someone else will.. If they then use their knowledge for evil we will be caught without any fishing line for the worms.

Whatever our scientist can think of there are others doing research along the same lines... for good and bad... Myself, I hope we one day have a really good understanding on how everything works.



posted on Oct, 17 2013 @ 05:48 PM
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reply to post by 727Sky
 


No problem Sky. I thought this was very interesting.
Especially the part about how a virus can more or less be stopped because of a codon sequence. Very interesting stuff indeed. There are a lot of implications in the article, mostly for good I believe.

Also I love fishing metaphors (fishing is kinda my thing) so you get a star for that lol.



posted on Oct, 17 2013 @ 05:52 PM
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reply to post by NowanKenubi
 


Well said.

Check out the quote from the article in the OP.


"This is a big step forward," says Steve Benner of the Foundation for Applied Molecular Evolution in Gainesville, Florida. "Once you have a cell that's able to handle your concept of DNA and your concept of amino acids, then you are opening up an entirely new field of science."



When science gets so complex and expensive as this, you know that all or the majority of the applications of this technology will be for profit. Scientists don't work for free, and once the information regarding these studies are kept as a trade secret, you only know, just like Nanotech, it will be used by our corporate overlords to suppress and exploit us.

This is a big step forward to what?
edit on 17-10-2013 by BlubberyConspiracy because: To what?



posted on Oct, 17 2013 @ 05:55 PM
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reply to post by CitizenJack
 


I just think that this stuff is to problematic to be done inside our biosphere this and robotic/automated duplicating nanotech should be banned from Earth, this could be a good motivator to start a lunar colony or even the habitation of Mars let them go crazy with genetics and nanotech in those "closed" environments but its too dangerous to risk a FUP here...



posted on Oct, 17 2013 @ 06:10 PM
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reply to post by Panic2k11
 


I can see the need for reservation. One has to just simply look at our past to see what happens when science goes all willy-nilly . Reckless science is no ones friend.

They did mention this


What's more, there's little threat of recoded E. coli swapping genes with its natural counterpart, were GROs ever to escape into the wild. Reassigned stop codons would be read as normal stop codons in natural cells, resulting in the premature termination of protein production. Preliminary studies also suggest that GROs cannot grow in the absence of the unnatural amino acid they've been designed to incorporate – adding another level of security.


However if you notice tho the word before threat is "little".
I does seem tho that we could potentially be able to create a mini biosphere (set to specifics) for these little guys to see how they grow and evolve on their own before unleashing the beast so to speak.
Then we could introduce unmodified bacteria to their biosphere and see what happen. That seems the responsible route to go. Outside of a moon lab which I would definitely prefer.



posted on Oct, 17 2013 @ 07:16 PM
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reply to post by CitizenJack
 


Life is not static and we still do not understand its workings to establish clear safety rules, from viral cross genetic transfer to mutations to the way bacteria share genetically information the door to something going wrong is very large.

Moving this industry off world (for stats) would be a great boost for economic sustainability of colonization and even help extraterrestrial industry, mining and terraforming,..
edit on 17-10-2013 by Panic2k11 because: (no reason given)



posted on Oct, 17 2013 @ 08:08 PM
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You know, there's an interesting (well, to me anyway) reason that there is redundancy in codons. It turns out that the ones that are redundant code for common mutations or repair errors. Generally, you'll see a redundancy when the repair enzymes screw up in a common way, and the redundancy will cover both the screw up and the correct repair. That way, you get the right amino acid regardless of the outcome.

If you remove the redundancies, you greatly increase the likelihood that you'll get a lethal error. They're there for a reason.



posted on Oct, 17 2013 @ 09:43 PM
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reply to post by Bedlam
 


I did not know that. That makes a lot of sense to build in a self correcting error , nature is a pretty efficient mechanism. Thanks for that tidbit I find it very interesting and wonder how this applies to the research.
edit on 17-10-2013 by CitizenJack because: (no reason given)
edit on 17-10-2013 by CitizenJack because: (no reason given)



posted on Oct, 17 2013 @ 11:02 PM
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reply to post by CitizenJack
 


Long ago when I took some grad level microbiology courses (it was for a project, don't ask), they went into some depth about it. I don't have my notebooks with me. Apparently, in some cases if you get a certain error or damage to the strand, the repair enzymes will sweep the strand repairing and/or excising errors, and in some cases it's obvious what the correction needs to be, and in others it's ambiguous. The enzymes will repair ambiguous errors but they have to guess at the correction. In that case, the redundancy covers you on most of the common mistakes.

You'd be AMAZED at the number and types of errors that occur, and at the complexity of the repair systems that are constantly zipping along and patching things back together. For instance, if you have a repeated sequence of T - T - T on one side, a UV photon can smack them apart so that instead of looking like this:

T - A
T - A
T - A

it looks like:

T A
| |
T A

That doesn't work anymore as a template for transfer RNA. So you have an excision enzyme that combs the strands looking for this all the time. If it finds it, it whacks them out, another enzyme then comes along and inserts a repair set of base pairs and patches the two ends back together. But it's ambiguous as to what side was T and what side was A. So you see that one as a redundancy.
edit on 17-10-2013 by Bedlam because: (no reason given)
edit on 17-10-2013 by Bedlam because: (no reason given)



posted on Oct, 17 2013 @ 11:22 PM
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wow. fascinating (and scary!) stuff.
Why do I keep thinking of Sonmi, one of the the 'fabricants' in Cloud Atlas?
(biologically designed to terminate without a certain substance) Yee
Interesting info, thanks for posting it!



posted on Oct, 17 2013 @ 11:29 PM
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Its just like script kiddies playing with something they don't understand...

Reverse-engineering is the name of the game in Genetics!!



posted on Oct, 18 2013 @ 03:52 AM
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Panic2k11
reply to post by CitizenJack
 


Life is not static and we still do not understand its workings to establish clear safety rules, from viral cross genetic transfer to mutations to the way bacteria share genetically information the door to something going wrong is very large.

Moving this industry off world (for stats) would be a great boost for economic sustainability of colonization and even help extraterrestrial industry, mining and terraforming,..
edit on 17-10-2013 by Panic2k11 because: (no reason given)


Wow thats a creative and very logical way to look at it. I wholeheartedly agree that we need to get our buts in space and start reaching out some more. This would provide such an incentive for so many industries . I realize most of the burden comes down to actually getting off our rock, gravity is a mean mean mistress...
However with out getting to political, the money we have been spending on wars and other interest probably could have gone towards reaserch into better propulsion methods to get off earth... Jus sayin.
Currently the price tag is around 10,000 a pound.
Or 16072.47 for a kilo (for the silly europeans
)



posted on Oct, 18 2013 @ 03:59 AM
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reply to post by Bedlam
 


I wonder if thats supposedly why these bacteria can't really survive outside of the environments they are raised and manipulated in. It would seem to me that the bacteria in our normal environment would reject these all together.
Maybe thats why they are confident there is little risk. Hmm..
All I know for sure is you are more knowledgeable than I in these matters than I.
Thank you for the lesson. As they say knowledge is power.



posted on Oct, 18 2013 @ 10:03 AM
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CitizenJack
reply to post by Bedlam
 


I did not know that. That makes a lot of sense to build in a self correcting error , nature is a pretty efficient mechanism. Thanks for that tidbit I find it very interesting and wonder how this applies to the research.
edit on 17-10-2013 by CitizenJack because: (no reason given)
edit on 17-10-2013 by CitizenJack because: (no reason given)


Your reply here reminds me of a mystery I have not been able to yet resolve. It's a mystery concerning the thinking process behind statements like the one you made. You probably didn't mean it in this sense, but a lot of people certainly do.

Why do people talk about nature like it is a conscious force? A tangible, constantly acting force, that drives our progression. But not only that, people who talk about it in this sense are often the most DIE HARD ATHIESTS and anti-religious personalities I know. According to our beloved current scientific paradigm (wouldn't want to upset that on here), all our progress to this stage by the 'natural' process of evolution was ACCIDENTAL. That correction mechanism isn't there for efficiency, nope, it's an accident (like the millions of other accidents upon accidents upon accidents) that nature churned out that actually turned out to not only be useful but light years ahead of anything we, CONSCIOUS/THINKING HUMANS, have done.

In fact, EVERYTHING nature has 'accidentally' or 'naturally' done is mostly light years ahead of us. Remember, we are conscious. Nature isn't conscious, it's a number running machine if anything. That number running machine created the most impressive thing in the entire universe - our body - along with a genius 3-DIMENSIONAL 4-BIT CODE called DNA. Let's not forget this amazing computer code has existed for possibly billions upon billions of years, and nature seemingly didn't have too much trouble implementing this, or should I say nature didn't have too much trouble accidentally scrambling a bunch of atoms together in a very impressive way. We, on the other hand, as conscious, rational and to be honest GOD-LIKE creatures in comparison to unconscious, non-driven and accidental nature, took ~2 million years to get to the point where we can even make 2-DIMENSIONAL 2-BIT code, let alone spawn the biological brilliance that is our universe. We are only just now discovering the possibility of self-assembling machinery. This has taken us thousands of years worth of knowledge, blood, sweat and tears across a WHOLE RANGE OF DIFFERENT FIELDS, yet of course, nature accidentally created the most impressive self-assembling and REPRODUCING machine in the universe from pretty much day-1 of life, which has led to this - the human body. We could only DREAM of such an invention, regardless how far we are with physics/chemistry/electronics/computing/nanotechnology/manufacturing and so forth and so forth.

Remember, nature does all of this accidentally. Yeah, I know it sounds absurd sometimes, but remember guys, this is Darwinism! And we love Darwinism! Oh let's not forget, even though nature is a random number churning accidental machine that just happens to work alongside a platform that allows it to manifest in actual meaningful and progressive ways, given enough time ANYTHING WILL HAPPEN (but let's never ask what provides the probabilities and what assigns them to the corresponding events, besides the actual platform for these things to manifest on). That's our neat little way of wrapping up this ridiculousness.

(Btw that's one of my favourite sayings - 'oh it naturally happened', it's like a magic word that means no further understanding is required - it IS AS BAD of an excuse as just saying 'God did it', of course many would deny this strongly).

Why is 'nature' talked about in this way by some? They do it without even realising. My favourite example is hearing a stone-cold atheist talk about evolution and say things such as 'polar bears are white because nature knew to give them white fur in the arctic' LOL. This is ABSURD! People do it unconsciously most of the time, and you'd be surprised how many people aren't actually even aware that evolution (macro/genetical - doesn't matter) is COMPLETELY ACCIDENTAL. THERE IS ZERO DRIVING FORCE ACCORDING TO OUR UNDERSTANDING. NONE WHATSOEVER. At least this is DARWIN'S THEORY. Which many people defend to the grave. If you believe evolution works in another way (micro-evolution is a different story now, since we understand epigenetics now but macro-evolution still fails into the 'accidental' category) then you may as well be a creationist, since you are not anymore believing in our BELOVED DARWINISTIC view of life.

'Nature is efficient' - 'It makes sense for nature to do that' - 'Nature gave us this/gave that animal this'

Do people not realise, that by speaking of nature in this way, you are speaking of a creator/a designer/a GOD. You are speaking of it as a force that drives the progression of this universe. That CANNOT EXIST INHERENTLY by our understanding. Such an existence would be nothing less than a God.

Nature can't think, it can't plan, it can't implement improvements based on drawbacks. In fact, the more I think about it, the more I'm convinced that everyone actually believes in a creator, except for they use the words nature and put it down to genetics and evolution, and that makes them feel good because that way they are not one of those 'silly religious nuts believing in fairy tales'.

Regardless, I am not here to promote or demote any ideas of natural evolution/spirituality/or any form of creationism.
I am merely just commenting on something I see a lot. Once again, not directed specifically at you, but the way you worded your sentence reminded me of this irk I have. I am a believer of evolution, though I believe Darwin was wrong (perhaps not fully aware would be a better phrase) about a few things, and I believe evolution MIGHT BE a process fundamentally ingrained into our universe, much like the fundamental forces in physics, rather than a fanciful word for a series of accidents following apparent miracles (original formation of the unbelievable manufacturing and factory production we call simple life, or even the building blocks of life themselves, or even the genetic code and so forth and so forth), that science is still explaining one step at a time going backwards billions of years.

The thing about science (I love it, I hold a Masters in Engineering), is that once we discovered it we pretty much dismissed all other ideologies we had, and started fresh. It's a catch up game now. The 'how' eventually will hit a wall and curl back up into a 'Why'.

On another note; that study is sheer brilliance. The schematics of this system we call life are truly beautiful, yet I worry that we are aiming to have more control over it than we should. The realm of creating and configuring species in whole new ways should probably be left to our virtual worlds (games won't be too far off the grade of detail of our universe soon enough). The potential for good is great, but the potential for bad is very worrying. But hey ho, who am I to complain. A mere single human, what progression can I alter.

Peace
edit on 18-10-2013 by DazDaKing because: (no reason given)
edit on 18-10-2013 by DazDaKing because: (no reason given)[/editb[edit
edit on 18-10-2013 by DazDaKing because: (no reason given)
extra DIV



posted on Oct, 18 2013 @ 04:24 PM
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reply to post by DazDaKing
 


# I must've been flipping bored when I wrote all that. Ignore my sarcastic ramblings lol, but seriously is it just me who notices other people do do that? Maybe I'm just surrounded by closet creationists
This is why I have to keep an agnostic viewpoint.

Back on topic though, I'm noticing these biological progressions happening very quickly recently, we're actually going to be able to successfully make DNA for anything we want at this rate - literally the key to life. Knowing how the world is right now with that ability I could picture military or big corps even making slave races/clones for just work. It'll be like the Sumerian Annunaki story all over again...

Or we could also use that knowledge to cure any genetically related problem, heal eco systems and create new ones, we could make an intelligent race and treat them right, theyd be superior to us though eventually. Theres a parallel there with our inorganic timeline - AI and robotics. Maybe even immortality depending on how deep our manipulation of the building blocks gets...maybe.

Still, leave it to the virtual world for now. Worlds not in the right shape right now. These technological advancements need a unified and equal race, or a race with rulers who genuinely are all about helping and progressing all of humanity with our technological advancements, which is also unified. We are nowhere near either of those! If restricted to only helping with conditions and diseases I'm all up for it.



posted on Oct, 18 2013 @ 06:36 PM
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reply to post by DazDaKing
 


As the Aussies would say, No worries mate.

I actually enjoy having conversations like that for the benefit of discussing ideas and beliefs. Anything that can open up meaningful discussion is great. You made some great points that I actually consider to be on track with certain beliefs I hold.

I dont belong to one club when it comes to creation and evolution, I admit that I'm just a normal guy who can barely grasp the idea and working of this grand thing called the universe. I'm along for the ride and want to learn and observe as much as possible while I'm here. I believe thats why some folks come to a place like ATS.

Currently I believe the that the truth between creation and evolution may actually lay somewhere in between, but I dont know this to be fact so I'm going to keep turning over stones and keep searching like the rest of my fellow humans.

Thanks for generating an interesting convo.





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