Darwinian evolution shown in Synthetic DNA

[Panonadin]

I thought this was very interesting, and I didn't see a link to it yet. Maybe I suck at searching.

http://news.nationalgeographic.com/news ... e-science/

[lutzj]

I might be misunderstanding the article (and the article might be misrepresenting the paper, which in turn might be misinterpreting the experiment...), but apparently the synthetic DNA "XNA" is only able to replicate by translating into DNA and then back again later. I'm not sure this reveals anything new about the molecule.

[maybeagnostic]

Yeah, the article is a little misleading. Not only do people need to copy the XNAs to DNA and back again for 'reproduction', the experiment actually uses artificial selection (the scientists picked the ones they liked the best, had them 'reproduce' and killed off everything else) instead of natural selection. It is still pretty cool though- they created six alternatives to DNA and RNA.

[yurell]

How is artificial selection different to natural selection? Traits that are best suitable for the survival of the species given the pressures present (in this case, the scientists) propagate, while those that are disadvantageous don't. I honestly don't see why the difference is a big deal (or a deal at all) ... it's just another selection pressure in the environment (of which we are a part).

[maybeagnostic]

Maybe I am just too used to the idea of evolution through natural selection. Artificial selection implies a purpose and direction to the changes and... uh, that would still be called evolution I guess.

Edit: Ah, it's in the title of the article.

Synthetic DNA Created, Evolves on Its Own

That strongly implies natural selection was used except it wasn't. Also they keep referring to the capacity for "Darwinian evolution" which means natural selection except I guess they never actually say that's what the scientists did.

[Shivahn]

How is artificial selection different to natural selection? Traits that are best suitable for the survival of the species given the pressures present (in this case, the scientists) propagate, while those that are disadvantageous don't. I honestly don't see why the difference is a big deal (or a deal at all) ... it's just another selection pressure in the environment (of which we are a part).

Well, an equally good question is "how is artificial different from natural?"

(Which is to say, you're entirely right, humans just like erecting walls and categorizing everything into neat boxes, regardless of how useful the boxes are or how well the things fit)

[addams]

I loved the article! What fun!

Of course, it goes from XNA to DNA and back again.
That is how these things work.

How stable is XNA? More or less than RNA? Between RNA and DNA or out in a different set altogether?

Some people get to have so much fun.

From the article:
"The team—led by Vitor Pinheiro of the U.K.'s Medical Research Council Laboratory of Molecular Biology—then evolved enzymes, called polymerases, that can make XNA from DNA, and others that can change XNA back into DNA."

Some people develop an eye for it. I, really, can't tell one bunch of goo from the next.
Does it look different to the unaided eye?

I, sometimes, wonder what we do some of this weird stuff for. Making synthetic genetic material? We don't have enough genetic material lying around? No.. We need some more. Something new and interesting.

I can barley do RNA->DNA->RNA. AIDS sure knows how to do it. The common cold is a good little Retro virus.
http://en.wikipedia.org/wiki/Retrovirus
That is, just, good clean fun.


Think of the Children!
This would add a whole other bunch of stuff they would 'Have To' know.
How do the sugars get replaced and Where is the electric charge that is holding all that together? The poor sweet things.

Replacing the large sugars with polymers is genius if, it is true.

Spoiler:

http://www.youtube.com/watch?v=ZGHkHMoyC5I
http://www.youtube.com/watch?v=7oaoOUpMswc
So, boring.

http://www.youtube.com/watch?feature=en ... epoOHYtH6g

The goo? Nope.
http://www.youtube.com/watch?feature=en ... wpTJVWra7I

[ahammel]

How stable is XNA? More or less than RNA? Between RNA and DNA or out in a different set altogether?

More stable than RNA, at least. RNA isn't unstable because of its chemical structure, it's unstable because the entire world is awash in enzymes that degrade RNA. Since it's single-stranded, I imagine it would be less stable than DNA, but that doesn't really matter because, from a molecular biologist's perspective, DNA is ridiculously stable anyway.

@maybeagnostic: I think it's misguided to say that their experiments don't demonstrate the capacity for natural selection in HNA. Sure, they set up the selection pressure artificially, but if you want to say that that doesn't count, you pretty much have to throw away the entire field of experimental evolution.

Likewise, it's not accurate to say that XNA can evolve on its own, as there's no XNA->XNA polymerase. I think the results basically mean that if you want certain traits from an XNA oligomer it's feasible to set up a selection pressure for those traits and evolve them.

[addams]

How stable is XNA? More or less than RNA? Between RNA and DNA or out in a different set altogether?

More stable than RNA, at least. RNA isn't unstable because of its chemical structure, it's unstable because the entire world is awash in enzymes that degrade RNA. Since it's single-stranded, I imagine it would be less stable than DNA, but that doesn't really matter because, from a molecular biologist's perspective, DNA is ridiculously stable anyway.

@maybeagnostic: I think it's misguided to say that their experiments don't demonstrate the capacity for natural selection in HNA. Sure, they set up the selection pressure artificially, but if you want to say that that doesn't count, you pretty much have to throw away the entire field of experimental evolution.

Likewise, it's not accurate to say that XNA can evolve on its own, as there's no XNA->XNA polymerase. I think the results basically mean that if you want certain traits from an XNA oligomer it's feasible to set up a selection pressure for those traits and evolve them.

What would you ever want? See? I am one of those.

What can you make XNA do that DNA and RNA can't do?

DNA and RNA do a lot. My mind is locked. It is cool. No doubt. I would love to see some. Does it look different. Is it slick not slimy?

But; What can it do? What will it ever amount to, when it grows up.

[ahammel]

What would you ever want? See? I am one of those.

What can you make XNA do that DNA and RNA can't do?

DNA and RNA do a lot. My mind is locked. It is cool. No doubt. I would love to see some. Does it look different. Is it slick not slimy?

But; What can it do? What will it ever amount to, when it grows up.

I can think of a couple of molecular biology situations where you might want something that's exactly like RNA only more stable. The authors also claim biotech and materials science applications, but they're vague about it.

It's nothing earth-shattering, but it's pretty neat.

[addams]

What would you ever want? See? I am one of those.

What can you make XNA do that DNA and RNA can't do?

DNA and RNA do a lot. My mind is locked. It is cool. No doubt. I would love to see some. Does it look different. Is it slick not slimy?

But; What can it do? What will it ever amount to, when it grows up.

I can think of a couple of molecular biology situations where you might want something that's exactly like RNA only more stable. The authors also claim biotech and materials science applications, but they're vague about it.

It's nothing earth-shattering, but it's pretty neat.

O.K. I'm dumb. When do you want something, just, like RNA only more stable?

Spoiler:

DNA->XNA->DNA?
The XNA part does trickses? Purple? Insert purple gene?
Poof. Purple people. (Burqas are looking better and better.)

Very Frankenstein meets Quasimodo.
http://en.wikipedia.org/wiki/Frankenstein
http://en.wikipedia.org/wiki/Quasimodo.

Can it make cute lab mice? Purple ones. Red, like Red corn. Ones with big Purple Ears and and orange faces?

Can it make a funny bacteria. Polymer for sugar? does it Eat Plastic? Is this it? The Plastic eating bacteria the environmentalist have been praying for?

I live in a plastic world. If, that thing got loose, well; shit would fall apart faster than we are used to. Not a really bad thing. I don't know.

We have been living with wood and rock eating Bacteria for a while now. Things seem manageable.

[Angua]

There are a couple of new drugs in develop (mainly aimed at interfering with viruses/bacteria) which use RNA that has been altered. The idea being that they are trying to interfere with their replication processes (which generally require RNA to be used by the enzyme at some point), so this RNA gets in there, but because it can't be broken down, clogs up the machine. (Sort of imagine putting tissues instead of toilet paper down the toilet - toilet paper is designed to dissolve, so won't clog up, but tissue is much stronger, even though they're both made of the same things).

[addams]

There are a couple of new drugs in develop (mainly aimed at interfering with viruses/bacteria) which use RNA that has been altered. The idea being that they are trying to interfere with their replication processes (which generally require RNA to be used by the enzyme at some point), so this RNA gets in there, but because it can't be broken down, clogs up the machine. (Sort of imagine putting tissues instead of toilet paper down the toilet - toilet paper is designed to dissolve, so won't clog up, but tissue is much stronger, even though they're both made of the same things).

I prefer the plastic eating bacteria. What the world needs. Right?
If, we don't have one, we need one.

There would be a sudden change in paradigm.
http://en.wikipedia.org/wiki/Paradigm

Spoiler:

Of course it will be made of plastic, its self. So; O to no nutritional value to life that depends on sugar. Right?

What fun! I wonder if shrimp will like them or think that they taste 'plasticy'.

Think of the changes in the food chain. Plastic eating bacteria are not a new idea. Loads of things wrong with them. But; We have so much plastic.

What happens in the very long run? It all settles down on the Ocean floor. A layer of plasticy, plastic eating bacteria to be found by geologists in the distant future.

Carbon 14, that. Where would the carbons be? Polymers.

I know squat about polymers and styrenes.
http://en.wikipedia.org/wiki/Polymer
http://en.wikipedia.org/wiki/Styrene

So; Yeah. You make more drugs as we attempt to use the ones we already have.
If, anybody gets that plastic eating bacteria off the ground, then, tell Me! I want to see it!

I think the ecosystem could handle it. We have shit that eats cellulose. This stuff would make cellulose a different way. Right?

Ech. God created ear buds for moments like this. The guy next door is blasting Rock and Roll. I used to do that when I worked, too. Sometimes. It was very different Rock and Roll.

Eww. This stuff is so dark and rough. Maybe; What I was listening to was not Rock and Roll.

(Shrug.) A God awful noise by any other name.....

[yurell]

How about nylon-eating bacteria?

[addams]

How about nylon-eating bacteria?

Yeah! How far is it from Nylon to Plastic? Kind of, depends on the kind of plastic. Right?

Spoiler:

Nylon.
http://en.wikipedia.org/wiki/Nylon
Plastic
http://en.wikipedia.org/wiki/Polystyrene

Those guys have a naturally occurring nylon eating pond scum! Those guys are so lucky! And; They are smart enough to know what they have. So, cool.

I like pond scum, sort of. It is slippery.
How did they figure this out? One more time through the article for me.
What? Did they take and grow out a sample every week?
Every month? Every year?
What made this little guy look different to some guys in Waders?

That is some hard Micro those guys are doing.
All I know about Micro is !LABEL EVERYTHING!

The Autoclave is our friend.

[Ormurinn]

Yeah! How far is it from Nylon to Plastic? Kind of, depends on the kind of plastic. Right?

Nylon is a polymer. Plastic is a kind of deformantion :p

Ok, nylon is a plastic by the common definition.

I can't weigh in with anything substantial on this topic as my biology is poor, but this seems like really cool news

[addams]

Yeah! How far is it from Nylon to Plastic? Kind of, depends on the kind of plastic. Right?

Nylon is a polymer. Plastic is a kind of deformantion :p

Ok, nylon is a plastic by the common definition.

I can't weigh in with anything substantial on this topic as my biology is poor, but this seems like really cool news

Well; It is fun reading.

"Jewish Fur Trader Hypothesis"

Is this funny news? I think that it is funny. One Jew was trading and fucking his way through Quebec. It, just, strikes me as funny.
It is a Hypothesis that has been proven wrong. It is still entertaining.

What would the Reality of that 'truth' be like? It could have happened. It, just, didn't.

Spoiler:

http://en.wikipedia.org/wiki/Tay-Sachs_disease#Signs_and_symptoms

I end up wandering around in the back fourty of Wikipedia. The strange things I learn.

http://en.wikipedia.org/wiki/Frame_shift_mutation
Not a completely new idea.

"Scientists have also been able to induce another species of bacteria, Pseudomonas aeruginosa, to evolve the capability to break down the same nylon byproducts in a laboratory by forcing them to live in an environment with no other source of nutrients."

Poor little bacteria. Evolve or die. Seems so mean. It does produce results. Or; So they say.

So, Off Topic

Spoiler:

We have a mushroom that eats Nuclear Waste! Are you surprised?

http://en.wikipedia.org/wiki/Radiotrophic_fungus

"These were first discovered in 2007 as black molds growing inside and around the Chernobyl Nuclear Power Plant.[1] Research at the Albert Einstein College of Medicine showed that three melanin-containing fungi, Cladosporium sphaerospermum, Wangiella dermatitidis, and Cryptococcus neoformans, increased in biomass and accumulated acetate faster in an environment in which the radiation level was 500 times higher than in the normal environment."

We? What do I mean we? I don't have one. What kind of a cage do they have for that thing?

It seems that they have some in NYC. They can, just, go over to Three Mile Island for food for it.
http://en.wikipedia.org/wiki/Three_Mile_Island_accident

Nice drive for mold food.

I have no idea if one thing that I read on the internet is true or not. How would ya' know?

[yurell]

I have no idea if one thing that I read on the internet is true or not. How would ya' know?

Follow the claim back to its source and treat everything critically.

[ImagingGeek]

O.K. I'm dumb. When do you want something, just, like RNA only more stable?

Some have mentioned potential experiment/drug uses. However, the goal in many of these sorts of "alternate genetic material" experiments is to identify possible genetic materials that may have preceded RNA/DNA during abiogenesis. Likewise, those interested in astrobiology are interested in these studies, as they point towards other viable options for non-earthly life.

There are also companies/groups seeking to create purely synthetic life (Craig Venter owns on such company). "Alternate" genetic materials are attractive to these groups, because they are patentable.

Bryan