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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

#121

Post by arximboldi »

fatboy93 wrote: post #112
_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…

> 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. That's the premise of Jurassic Park 1, except with an amino acid.

There is this soviet science fiction story with a similar premise, but self-replicating machines:

Crabs On The Island (Russian 1958, English 1968) (original: Kraby idut po ostrovu), by Anatoly Dneprov

http://arvindguptatoys.com/arvindgupta/15r.pdf

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

#123

Post by colordrops »

RHSeeger wrote: post #107
colordrops wrote: post #52

Earlier quoted context omitted.

No, GMOs are inherently safe and you are anti-science /s

GMOs are not inherently safe, they're just not inherently unsafe. It's possible to create something devastating to the environment, but it's also possible to create wonderful things. The trick is being careful to create the right things (which, given how companies work, generally means regulation).

I fully agree, which is why I added the /s(arcasm) tag at the end. Not sure if that is commonly understood here on HN. I was just saying that frequently comments that imply even the slightest criticism about GMOs get attacked as anti-science, which is absurd.

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

#124

Post by dnautics »

vivekd wrote: post #97
dnautics wrote: post #91

Earlier quoted context omitted.

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 cor…

correcting does happen at the tRNA stage and it's not as trivial as one might think[0], but the technology to incorporate unnatural amino acids using reengineered stop codons has been around for a while and presumably it will work with X and Y. Note that Romesburg (author of the DNA paper) was a postdoc in the Schultz lab, where he was originally working on this DNA stuff -- I was across the street > 10 years ago when they first got the DNA stuff to work in vitro. He got his own lab across the street and continued on the DNA stuff (but also other things).

e coli: http://www.nature.com/nmeth/journal/v3/n4/full/nmeth864.html

yeast: http://link.springer.com/protocol/10.1007%2F978-1-61779-331-...

mammalian cells (very very very very very hard): http://www.nature.com/nmeth/journal/v4/n3/full/nmeth1016.htm...

[0] the trick is to steal a tRNA from an archaeon; scuttlebutt is that the postdoc on the paper stole the idea from the lab across the hall, which was actually working on that archaeon.

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

#125

Post by [deleted] »

sbmassey wrote: post #56
portent wrote: post #53

Earlier quoted context omitted.

OK, well we can always say that the heat-death of the universe renders all problems irrelevent, but it's a bit of a cheat in my opinion. The original poster seems to imply that knowing the code means that you can know the behaviour of the system; I do not think that is the case, and my simple (chaotic) example tries to demonstrate this.

Well indeed, as per Turing on the Entscheidungsproblem one cannot know what some abstract bit of code does without running it, but one can sometimes put limits on its behaviour - your snippet will never do anything but print out numbers, for example, or something running under seccomp might be prevented from making certain syscalls.

[deleted]

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

#126

Post by TeMPOraL »

Retric wrote: post #113
portent wrote: post #76

Earlier quoted context omitted.

What you are saying sounds intuitively true, but the mathematics of Chaos Theory showed that it is not actually the case. What my code snippet is doing is running a sample of a particular chaotic function that was originally inspired by biology (a simple predator/prey model). Ultimately, what happens is that you just cannot predict how the function will behave - it is chaotic. Ultimately most complex systems start to…

No, virtually is the important bit. In code we can know all the details. So, you can predict the code just fine. For example running it twice and getting the same output the second time. Chaos theory is based on real world systems that can't be measured accurately. However, internal computer simulations don't have that limitation. One example is if you try saving a simulation to disk you need to copy all internal sta…

You're right (and I think commenters saying that parent was talking about halting problem are wrong - it was clearly about chaotic systems, which are deterministic). And yet, this doesn't make the original statement - "we have no idea what happens in our own code" - any less true. Without even touching the halting problem, all code we write quickly explodes in complexity beyond our ability to mentally simulate it, and those of us who don't work on life critical systems are not paid for anything more than some unit tests and a cursory "uh, it looks ok to me" assessment.

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

#127

Post by TeMPOraL »

colordrops wrote: post #123
RHSeeger wrote: post #107

Earlier quoted context omitted.

GMOs are not inherently safe, they're just not inherently unsafe. It's possible to create something devastating to the environment, but it's also possible to create wonderful things. The trick is being careful to create the right things (which, given how companies work, generally means regulation).

I fully agree, which is why I added the /s(arcasm) tag at the end. Not sure if that is commonly understood here on HN. I was just saying that frequently comments that imply even the slightest criticism about GMOs get attacked as anti-science, which is absurd.

I hope, though, that you understand that this is basically a reaction to GMOs being assumed inherently dangerous and evil by the general population, by the virtue of not being "natural" enough.

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

#129

Post by B1FF_PSUVM »

jcoffland wrote: post #46
Joeri wrote: post #15

Earlier quoted context omitted.

Then again, nobody knows how skynet will get started. If it does happen, you can be sure it'll be done by someone who is sure that things just don't work that way, right up to the moment they are crushed by a giant metal boot.

Let's hope that Skynet is not able to feed off of spam. There's so much of it's food already. We'd never be able to stop it.

I expect that 'Skynet' will be descended from spambots.

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

#130

Post by jcoffland »

darkmighty wrote: post #120
Retric wrote: post #113

Earlier quoted context omitted.

No, virtually is the important bit. In code we can know all the details. So, you can predict the code just fine. For example running it twice and getting the same output the second time. Chaos theory is based on real world systems that can't be measured accurately. However, internal computer simulations don't have that limitation. One example is if you try saving a simulation to disk you need to copy all internal sta…

What about the following? x=5 y=5 while True: if y%2 == 0: y=y/2 else: y=3y+1 if y == 1: x=x+1 y=x if y==x: return x Please predict the code. I'll even give you $500 in memory of some guy named Erdos if you get it right (and I haven't even gone for a provably undecidable example! :) ) PS: Don't waste time checking x values less than 1000000000000000000

It will run in a loop until someone turns it off. How do you want to pay up? I accept cash and Bitcoin.
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