Deformities Alarm Scientists Racing to Rewrite Animal DNA • Hacker News Board

Re: Deformities Alarm Scientists Racing to Rewrite Animal DNA

#111

Post by monocasa » Sat, Dec 22, 2018, 8:38 PM UTC

jf- wrote: post #68

andrewflnr wrote: post #62

Earlier quoted context omitted.

DNA is almost exactly machine code. It's directly executed by ribosomes and other cellular machines. Of course there are no guard rails.

Except that it doesn’t represent logic, it represents strings of amino acids that form proteins that fold up in unpredictable ways and interact with lots of other things to do stuff that half the time is weird and inefficient and doesn’t make sense.

There's quite a bit of logic encoded. DNA has equivalents of conditional jumps, and stored state. That's in the stuff that for a long time was called "junk DNA" between the encoding sequences.

Re: Deformities Alarm Scientists Racing to Rewrite Animal DNA

#112

Post by rjf72 » Sat, Dec 22, 2018, 8:38 PM UTC

htk wrote: post #70

jayalpha wrote: post #65

Earlier quoted context omitted.

"No single point just does a single thing." Exactly this! And this is why GM foods are more dangerous than you might expect. Even if gene x does only x in organism A, there is no guarantee that gene x does only one thing or the same thing in organism B.

Even if this hypothesis is correct, I would replace "dangerous" with "unpredictable", because the resulting effects of those interactions would be as likely to cause good as to cause harm.

Why do you think changes would be as likely to cause good as to cause harm? In complex, yet structured, systems - I think changes without fully understanding what you're doing are vastly more likely to cause harm than good. Software is the obvious example. Change a line of bytecode/assembly to something else. I think the chances of that change being good are extremely close to 0.

Re: Deformities Alarm Scientists Racing to Rewrite Animal DNA

#113

Post by trophycase » Sat, Dec 22, 2018, 8:38 PM UTC

laretluval wrote: post #82

What's the agenda behind the spate of gene editing alarmism lately? The article cites the July Nature Biotechnology article about unintended consequences of CRISPR-Cas9 but subsequent work has eliminated many such consequences using slightly different techniques. No word of that fact in this article. If consequences of genetic engineering are poorly understood, then this isn't reason to worry about reckless research.…

I definitely don't want barriers on research. Rather, the issue is that this technology is being used by overzealous profiteers who likely care very little about potential consequences. Alarmism is warranted IMO when corporations that have proven to be sociopathic are using this technology and potentially affecting near every in the country (and maybe the planet). Haven't we learned anything from global warming?

Re: Deformities Alarm Scientists Racing to Rewrite Animal DNA

#114

Post by salawat » Sat, Dec 22, 2018, 8:39 PM UTC

sleepydog wrote: post #37

Valmar wrote: post #9

Earlier quoted context omitted.

Indeed. DNA is the most fucking complex and complicated programming language. We have barely any understanding of how the whole thing hangs together, let alone how it's parsed and written, and how it all translates from stem cells to whole organs, an immune system, the complex interrelation between organs, the nervous system, the whole gamut. And that's not even touching on the nature of mind and consciousness in rel…

It's like if you had a version of C that replaced all compilation errors with undefined behavior.

Not really. It's more like a compiler, an optimizer/simulator, and compiler-compiler all pipelined in a circle. Seemingly random changes get incorporated into a starting binary that are selectively pruned/modified during the simulation/optimization phase, which generates a new compiler-compiler, which constructs a new compiler, which generates a new binary to run through the optimzer again.

It's more in-depth, because I'm abstracting away the elegance of protein/enzyme selection and translation through biochemical/mechanical fitness... But it's all there.

I'm just afraid of the predilection humanity as a collective has for not taking into account/being able to reason through higher order network effects.

Our economic/environmental woes prove that anything approaching the periodicity of a human lifespan becomes extremely hard to analyze/predict in any meaningful way. It seems to work though... So some days I feel like I can't really frame an argument against it.

It's kind of hard to argue that it isn't working when you have air conditioning.

Re: Deformities Alarm Scientists Racing to Rewrite Animal DNA

#115

Post by chiefalchemist » Sat, Dec 22, 2018, 8:41 PM UTC

cronix wrote: post #57

From my laymans POV, DNA is just a shit ton of variables in a very complex code that interact with each other. No single point just does a single thing. They all interact with each other. No different than changing a variable in one piece of code and having it create a bug in another that was previously working. For me, the real scary part is altering something, which inadvertently changes something else that isn't q…

That's not only a layperson's POV. There was an article in The Atlantic (approx a year+ ago) - which I've looked for an cannot find (sorry) - on a scientist who long to short "I don't think things (i.e., DNA) are what most science thinks it is." Much like you he said, "it's not this simple. the mesh is more complex and has multiple currently unforeseen dependencies." Obviously, I'm paraphrasing.

And every month since I've read something that supports this and undermine the current conventional wisdom / proof.

Re: Deformities Alarm Scientists Racing to Rewrite Animal DNA

#116

Post by danieltillett » Sat, Dec 22, 2018, 8:42 PM UTC

feistypharit wrote: post #101

cronix wrote: post #57

From my laymans POV, DNA is just a shit ton of variables in a very complex code that interact with each other. No single point just does a single thing. They all interact with each other. No different than changing a variable in one piece of code and having it create a bug in another that was previously working. For me, the real scary part is altering something, which inadvertently changes something else that isn't q…

Or the really scary part...if it not noticed for generations. For example, a reduction of IQ each generation or such.

Very droll. Nice elude to dysgenics [0].

0. https://en.m.wikipedia.org/wiki/Dysgenics

Re: Deformities Alarm Scientists Racing to Rewrite Animal DNA

#117

Post by lukeschlather » Sat, Dec 22, 2018, 8:44 PM UTC

dwaltrip wrote: post #94

smaddox wrote: post #69

Earlier quoted context omitted.

GM foods are arguably no more dangerous than any massively engineered foods we've been eating for decades/centuries. Direct gene modification is more like using a scalpel rather than a 2x4. Still potentially dangerous, but far more precise.

It's more like editing the raw binary of an executable. It's only more precise if you understand the binary representation and the impact of changes. Otherwise it's incredibly imprecise, as you are just randomly flipping switches. In the case of genetics, we have a some understanding, but it is fairly limited. There is real potential for unexpected harm, given how much we don't know and the complexity of the code. Of…

I don't think it's really accurate to describe selective breeding as restricting how you can modify the underlying data. I'd rather say that the executable itself contains layer upon layer of consistency checks so if you modify it too much it will just refuse to "boot up." In fact selective breeding relies heavily on this mechanism since it can create hundreds or even millions of nonviable organisms for every viable organism.

If the consistency checks in the natural genome don't stop you, pretty much by definition whatever you're doing could happen through an unlikely coincidence of selective breeding (especially if you involve a wild virus to take the place of the lab virus.)

Re: Deformities Alarm Scientists Racing to Rewrite Animal DNA

#118

Post by anigbrowl » Sat, Dec 22, 2018, 8:51 PM UTC

I'm no biologist but I don't feel like we have a good enough theoretical understanding of DNA, in the same way that doing search and replace on object code in a hex editor doesn't mean you have a good understanding of programming. The little I know about systems biology from using Cytoscape and reading a few papers reminds me of learning to use a disassembler instead of a debugger.

Re: Deformities Alarm Scientists Racing to Rewrite Animal DNA

#119

Post by anigbrowl » Sat, Dec 22, 2018, 8:53 PM UTC

akira2501 wrote: post #108

cronix wrote: post #57

From my laymans POV, DNA is just a shit ton of variables in a very complex code that interact with each other. No single point just does a single thing. They all interact with each other. No different than changing a variable in one piece of code and having it create a bug in another that was previously working. For me, the real scary part is altering something, which inadvertently changes something else that isn't q…

> From my laymans POV It's just so much more complicated than that. There is an additional huge array of variables like introns[1] and exons[2]. There's also the fact that not all base pairs encode even for genes, there's things like tRNA[3] and ribosomes[4] and the super amazing ribozymes[5]. Even after all that you have specific DNA binding factors[6] that along with the insane machinery[7] of our DNA regulate whic…

C may let you shoot yourself in the foot, C++ may let you blow your whole leg off, but only CRISPR will let you turn it back into a tentacle.

Re: Deformities Alarm Scientists Racing to Rewrite Animal DNA

#120

Post by wolco » Sat, Dec 22, 2018, 8:56 PM UTC

notheguyouthink wrote: post #93

Valmar wrote: post #76

Earlier quoted context omitted.

GM foods are actually more dangerous, due to how GM works. Cross-breeding allows nature to combine things that fit together in all of the right places. And we just don't know how that even happens, or why. We don't understand nature's algorithm for DNA. No even the tip of the iceberg. Sure, nature isn't always correct, but does thing properly 99.999% of the time. And that's good enough. It is utterly incomparable to…

> Cross-breeding allows nature to combine things that fit together in all of the right place I feel like this is putting too much faith in "natural" methodologies. Eg, who's to say a cross breeding solution is less dangerous than a GM solution? If the concern is that it may take 50 years to know the GM is bad, why are we assuming the non-GM is good now ? You could say that people have been cross breading for many man…

I have a pear tree with three different types of pears on different branch. Grafting has been going on for centuries.

I think the fear around gmo is that food will be less healthy. The same way prepared food takes a few elements of food mixes with chemicals to get strong favours without the depth of flavour. They do this to save costs. GMO companies are making seeds that create plants that do not get eaten by pests. It sounds great until we realize those plants have a toxic substance inside that harms us.