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New organisms have been formed using the first ever 6-letter genetic code

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Re: New organisms have been formed using the first ever 6-letter genetic code

#91

Post by dnautics »

maxander wrote: post #80
vivekd wrote: post #72

So will this actually mean anything? Can adding extra letters to an organisms genetic code actually have the capacity to change it's attributes in any meaningful way. Every biological characteristic on the planet seems to have been achieved through using the same 4 molecules, will the addition of more molecules create new characteristics or be useful in any way?

Not really; essentially all DNA "really does" is code for RNA, which in turn codes for amino acid sequences that fold into proteins. As long as the RNA and amino acid libraries are the same, it's just representing the same stuff with a different set of symbols. In practice, it's probably going to be used as tools for manipulating organisms for experimental purposes, since scientists can do things to the synthetic bas…

The biggest application will be introducing unnatural amino.acids into proteins.

Re: New organisms have been formed using the first ever 6-letter genetic code

#92

Post by AnkhMorporkian »

astrodust wrote: post #90
AnkhMorporkian wrote: post #86

Earlier quoted context omitted.

I'd argue that any organism is inherently open source, just not necessarily free and open source.

If it's been baked the source is wrecked, so not really.

Ending a bash script in rm $1 doesn't magically make it not open source, just inherently self-destructive.

Re: New organisms have been formed using the first ever 6-letter genetic code

#93

Post by an-honest-moose »

AnkhMorporkian wrote: post #86
astrodust wrote: post #81

Earlier quoted context omitted.

The biggest problem is they're not open source. What went into making that organism? Is there a standard for documenting this and reasonable public disclosure when relevant? Foods have ingredient lists for a reason.

I'd argue that any organism is inherently open source, just not necessarily free and open source.

By that logic you could argue that software is inherently open source.

Re: New organisms have been formed using the first ever 6-letter genetic code

#94

Post by NeutronBoy »

jakeogh wrote: post #89
NeutronBoy wrote: post #83

> But Romesberg says there's no need for concern just yet, because for one, the synthetic base pair is useless. It can't be read and processed into something of value by the bacteria - it's just a proof-of-concept that we can get a life form to take on 'alien' bases and keep them. While it might not be useful to the organism, could the synthetic base pairs lead to a way to store data? Imagine a bacteria that can be u…

http://www.extremetech.com/extreme/134672-harvard-cracks-dna...

Yeah that's the sort of thing I'm thinking of! From my total layperson perspective, the OP article seems to be a step in the right direction for this.

Re: New organisms have been formed using the first ever 6-letter genetic code

#96

Post by tstactplsignore »

glenstein wrote: post #84
tstactplsignore wrote: post #65

Earlier quoted context omitted.

Difficult to see how this comment, as common as it is, is anything but unscientific. Biological systems are often highly predictable in many circumstances - in fact "biological predictability" is what accounts for the general success of all modern medicine and agriculture. If the field "cannot begin to claim we don't fully understand" things now, when do we reach the point where we suddenly "know enough to begin to d…

There's absolutely nothing unscientific about saying biology is hard to understand and predict relative to software. We understand some biology, but the complexity of things like the genome, brain function, bacteria, etc. is overwhelming. (Relevant xkcd: https://xkcd.com/1605/ ). Far from being antiscientific, it's a rather straightforward observation that borders on self evident. What would be unscientific would be…

Yes, it is a self-evidence observation that as a whole, we understand the software systems we've built more than the entirety of all biological systems. Obviously nobody is disputing that.

The original claim was that to against this research or cautious about this research "because we don't always predict what biological systems will do" is on the same order of magnitude analogous to claiming we should be against or cautious about people implementing machine learning algorithms because "we can't always predict what software will do, especially AI!". I believe that this comparison is 100% valid and useful for explaining why the original reasoning is flawed to those in computer science who are pretty uninformed on biology.

The actual "chances of something going wrong" might not be the same - it might be a 10^-25 chance that you made a mistake in your implemented SVM that, err, causes a catastrophic error that has serious consequences for humanity, possibly because "the internet is all connected, man" (if this sounds ludicrous to you, that is how the other side sounds to me on these cases of biology!) and a 10^-24 chance that this research results in some organism that, err, causes a catastrophic error that has serious consequences for humanity (it is equally difficult for me to envision this), but the point is that both are cases where we can be so confident that some absurd catastrophe will occur because we have studied .

If you have specific predictions about how on Earth this research could result in catastrophe, make them and we can discuss how possible they are. If not, it really is anti-scientific fear-mongering: you aren't making any positive claim about a legitimate possible issue, you are simply saying "I have this gut feeling that like something could go wrong with that and it could like spread and be bad", even though we have excellent reasons to assume this is not the case and no reason to assume it is, and that everyone with any field knowledge strongly disagrees with your personal assessment, and the situation really is analogous to the person worrying about the SVM.

Edit: And to further explain why this is "anti-science" - it is because you are not making any testable claims, you are simply saying "We don't know everything that can go wrong, there could be something you haven't thought of!" and using that impossible to disprove hypothesis to shut down research and development, e.g. the process of science itself.

Re: New organisms have been formed using the first ever 6-letter genetic code

#97

Post by vivekd »

dnautics wrote: post #91
maxander wrote: post #80

Earlier quoted context omitted.

Not really; essentially all DNA "really does" is code for RNA, which in turn codes for amino acid sequences that fold into proteins. As long as the RNA and amino acid libraries are the same, it's just representing the same stuff with a different set of symbols. In practice, it's probably going to be used as tools for manipulating organisms for experimental purposes, since scientists can do things to the synthetic bas…

The biggest application will be introducing unnatural amino.acids into proteins.

This is what I'm wondering about, can RNA meaningfully make proteins using an instruction manual that contains molecules that it doesn't recognize? The scientists created an organism with new DNA molecules but there is nothing in the paper about whether RNA is actually recognizing and transcribing these new molecules and how the result of that looks.

My guess is that it would be considered an error by the RNA and corrected but your parent suggest that the RNA is just treating it like it would one of the other four molecules with is also a possibility.

Re: New organisms have been formed using the first ever 6-letter genetic code

#98

Post by taneq »

_yosefk wrote: post #40
_throwaway1843 wrote: post #8

Star Trek depicted one of the scarier applications of such a technology: There, The Jem'Hadaar are a genetically engineered race of warriors controlled by the Dominion, who exert power over them by being the sole provider of a substance (Ketracel-White) that they need in order to survive: https://en.wikipedia.org/wiki/Dominion_(Star_Trek) http://memory-alpha.wikia.com/wiki/Ketracel-white If my reading of the paper is…

It's good as long self-termination is a nice-to-have feature. If you REALLY want them to self-terminate but you found out that they mutated and can now synthesize X & Y, you're in trouble. Genetically modified organisms are a bit scary, but genetically modified organisms that replicate autonomously are more than a bit scary. As programmers - a profession that managed to spread Shellshock, the dumbest imaginable backd…

> If you REALLY want them to self-terminate but you found out that they mutated and can now synthesize X & Y, you're in trouble.

There's a good hook for a sci-fi story. Some low-level manager in a biochem company starts siphoning off XY juice to sell on the black market, and doesn't realise that by slowly ramping up their thievery they're evolving the killswitch out of their engineered organisms...

Re: New organisms have been formed using the first ever 6-letter genetic code

#99

Post by CodeWriter23 »

eivarv wrote: post #79
_yosefk wrote: post #40

Earlier quoted context omitted.

It's good as long self-termination is a nice-to-have feature. If you REALLY want them to self-terminate but you found out that they mutated and can now synthesize X & Y, you're in trouble. Genetically modified organisms are a bit scary, but genetically modified organisms that replicate autonomously are more than a bit scary. As programmers - a profession that managed to spread Shellshock, the dumbest imaginable backd…

Genetically modified organisms are a bit scary... Why?

Because embedding new species into an untested environment can be devastating. My example is the accidental import of tree snakes to Guam, which resulted in the complete extinction of all birds on the island, because the snakes ate the eggs faster than the birds could adapt. There are numerous numerous other examples of accidental release of animals destroying ecosystems.

Re: New organisms have been formed using the first ever 6-letter genetic code

#100

Post by taneq »

portent wrote: post #50
jcoffland wrote: post #45

Earlier quoted context omitted.

> We have no idea what happens in our own code That's an overstatement. Sure code can be very complex but we actually can see exactly what's going on whenever we really want to. It's just that we cannot see what's going on with all the code all the time.

code can be very simple, and we don't always know what it will do. Simple example: can you tell me if this snippet of (python) code will ever terminate or not? x=0.5 while x 0.7: x=3.59*x*(1-x) print x ... and what if the 3.59 was replaced by a different number - maybe 3.60 ? or 3.84 ?

And this is a great illustration of why arguments that "humans are special because computers can never solve the halting problem" are specious. We can't solve the halting problem (in the general case) either.

That said, we can still see what that code does, even if we don't know precisely what code path it takes. Great example though!

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