XNA and other things genetic

[axordil]

So scientists have made DNA-type molecules, replacing the sugars with polymers:

Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.

That's the abstract from Science.

So apart from science-fiction consideration (I'm trying to work this into a story) this, combined with the new ability to use nucleic acids as ultra-dense archival memory, has all sorts of interesting implications.

[River]

And I know what I'll be downloading at work tomorrow...

People have been screwing around with modified bases and alternative backbones for a while. I wonder what these guys did that's different from what's already out there.

[axordil]

My impression is that they are close enough as structural analogs to fold and such like the Real Thing, so they're more durable than DNA. The enzymes that break DNA down don't affect them much.

From someone who's poking around the area for a story, the notion of alien life running on non-DNA genetic information storage is what catches my eye. All the SF stories about silicon-based life aside, I've never seen any indication that another molecule could carry that load for an organism of any complexity.

[Primula Baggins]

I don't know much about it, but the somewhat rusty molecular geneticist I have on hand says he thinks DNA will be a pretty common default in life found elsewhere.

As even a rusty chemist I do know that silicon-based life is very, very unlikely. Silicon is the same valence as carbon, but it's larger (weaker bonds, not enough stability for really long chains), and there are chemical differences that would make aspects of metabolism difficult (e.g., carbon dioxide is a gas that can be breathed or transpired out, and it isn't energetically hard to recover the oxygen by another metabolic pathway; silicon dioxide is sand, and it's so hard to get the oxygen back out of sand that that's where most of the oxygen on the planet is and will stay).

[River]

I'm a little wary of making any declarative statements about what is or isn't possible in an alien system. One of the reasons people are so stuck on DNA and RNA is that ribose and phosphate are thought to be as abundant elsewhere as they are on Earth. Also, DNA and RNA are very very well-suited to their jobs. But nature can and does boggle the human imagination on a regular basis and the selective pressures and available materials in an alien system could be completely unlike what we've had here. I do agree though that you're unlikely to find a life-form that isn't carbon-based. Nothing else on the table forms those long stable chains.

I'm also extremely wary of making any sort of statement about a paper I haven't read. So I'll sound off tomorrow about this result. People have, however, synthesized nucleic acid with peptide bonds as the backbone (PNA; guess it's still nucleic acid because the bases are the standard set) and they've also done some interesting things with "locked" sugars in the backbone (LNA). I.e., the sugars can't flip their pucker like they can in RNA and DNA. Also, they've modified the bases themselves - there's a company in Boulder that's very proud of itself for its modifications as they've been able to raise aptamers that bind far tighter than anything seen before. I believe the modified bases can be read by your typical DNA polymerase and utilized by your typical RNA polymerase. AFAIK, LNA and PNA are completely synthetic and I'm not even sure what they're used for. From the abstract ax posted, I am guessing that, given that he authors claim to have raised aptamers, they can get your standard crop of enzymes to bind and catalyze reactions with their new type of backbone. That would be extremely exciting. But I need to read the paper.

[yovargas]

Nothing else on the table forms those long stable chains.

Not that I know anything about anything but........maybe life elsewhere has figured out a way to do it with a wide variety of short chains instead of a couple long chains?

[Holbytla]

A nearly infinitely small, nearly infinitely dense and nearly infinitely hot speck of energy, explodes and creates every subatomic particle, atom, element, force, neutrino, planet, star, black hole, animal, Holby and galaxy.

I'm pretty sure most things are possible in the universe.

[Túrin Turambar]

I think its significant that no life that isn't carbon-based has been found on earth. If, say, silicon-based life were possible there's no reason that it couldn't have arisen here. And I can't see other planets being significantly different to earth in their original chemical make-up.

The answer to this question might lie either on Mars or Venus (in fossil form) or, perhaps more likely, on Europa. If we find evidence of life on these planets, then that would tell us a lot. Europa might be the best bet, as a probe could in theory zero in on heat sources indicative of geomethermal vents, but it's still a huge undertaking simply to satisfy our curiosity.

[Holbytla]

Lord_Morningstar

And I can't see other planets being significantly different to earth in their original chemical make-up.

It is remotely conceivable that the make-up of other planets in the universe, are astoundingly different from ours, and that there could be some form of life that we aren't familiar with, but at the same time it is highly unlikely that we would ever be able to meaningfully (something beyond radio or video waves) have any type of interaction with any life anywhere.
In this case, size does matter, and we are just too far away from anything.

Even if there were intelligent life near the closest star, we are talking travel time more than the average human life.

But this is straying way too far from the topic.

[Primula Baggins]

There's more to the question of life on other planets than satisfying our curiosity. Imagine being able to study how other forms of life, forming in an entirely separate environment, solved the same problems life on Earth faced. The results could have huge implications. Just the existence of life another world has huge implications, philosophical as well as scientific, even if it's just bacteria, or fossil bacteria as might be the case on Mars. (And I'm willing to bet we'll find a lot more than bacteria around those warm undersea vents on Europa.)

Of course, Mars life and Earth life might actually be related, seeded from one planet to another by meteorites. That's unlikely to be true for Europa.

Venus can't support life and I would bet it never has. The surface is the temperature of boiling lead at incredible pressures, and the clouds themselves are sulfuric acid. Life needs a mild, controlled environment, at least within the body and within the cell, in order to grow and replicate. It needs not to be burned to a crisp or oxidized by powerful acid. Liquid water and a source of energy. . . .

Some people theorize that life on Earth first formed down near our own undersea vents, when the surface was still being bombarded and had a poisonous atmosphere. It also at least used to be suspected that life may have been arisen on Earth several times, only to be smacked down by a catastrophic impact, before the form that led to us (among other things) escaped that and took hold.

[Impenitent]

I'm geeking out.

I never went further than first year chem and biology and have forgotten much of it, but this conversation is creating all kinds of joyful excitement in me. I don't know any place else where I could eavesdrop on this kind of discussion.

[Túrin Turambar]

There's more to the question of life on other planets than satisfying our curiosity. Imagine being able to study how other forms of life, forming in an entirely separate environment, solved the same problems life on Earth faced. The results could have huge implications. Just the existence of life another world has huge implications, philosophical as well as scientific, even if it's just bacteria, or fossil bacteria as might be the case on Mars. (And I'm willing to bet we'll find a lot more than bacteria around those warm undersea vents on Europa.)

As much as I like knowing more about the cosmos, I'm leaning to the position that the high costs of space exploration mean we should approach it with caution. Everyone is thrilled by the Curiosity rover, for example, but $2.5 billion dollars seems like a hell of a lot to me to bring back some (in my view) pretty unclear pictures of Mars. A world that we already know enough about to know that it doesn't have all that much to offer us any time in the foreseable future. And with the economic situation as it is now, and as it is likely to continue, the idea of manned Mars exploration strikes me as insane.

I don't think that we should stop sending these probes. The New Horizons mission to Pluto, for example, will bring us images that we've never seen before. But it may be that Europa is a dead world with ice running straight down to rock and the proposed undersea oceans nothing but science fiction.

At risk of heresy, I see space exploration in the same terms as building sports stadiums. Certainly a justifiable use of public money but hardly a priority.

Venus can't support life and I would bet it never has. The surface is the temperature of boiling lead at incredible pressures, and the clouds themselves are sulfuric acid. Life needs a mild, controlled environment, at least within the body and within the cell, in order to grow and replicate. It needs not to be burned to a crisp or oxidized by powerful acid. Liquid water and a source of energy. . . .

Wiki suggests that, at one point, Venus was much more earth-like and probably had significant amounts of liquid water. The runaway greenhouse effect only came later. Still, good luck to any attempt to fossil-hunt there.

Some people theorize that life on Earth first formed down near our own undersea vents, when the surface was still being bombarded and had a poisonous atmosphere. It also at least used to be suspected that life may have been arisen on Earth several times, only to be smacked down by a catastrophic impact, before the form that led to us (among other things) escaped that and took hold.

I think it likely that life on earth arose several times (I wouldn't be surprised if photosynthesis and chemosynthesis had different origins). The way in which these life forms are similiar suggests to me that life on other worlds would share many of those similarities.

[axordil]

One of the things about it that's relevant for my story is that the most efficient method for storing genetic information really does seem to be genes. If you wanted to bank the genetic code of everyone on the planet, you could fit the requisite DNA in a coffee cup...so coming up with a long-term stable version would be very helpful for my plot, which involves moving a lot of genetic information to another planet.

Beyond that, though, the idea that there's a molecule that replicates the functionality of DNA that doesn't exist in nature (that we know of) raises the issue of whether it could exist in nature elsewhere.

[vison]

A nearly infinitely small, nearly infinitely dense and nearly infinitely hot speck of energy, explodes and creates every subatomic particle, atom, element, force, neutrino, planet, star, black hole, animal, Holby and galaxy.

I'm pretty sure most things are possible in the universe.

Read "Dragon's Egg" by Robert Forward. It's about intelligent life - the Cheela - evolving on a neutron star. It's about the best scifi novel I've ever read and I have read a lot.

[River]

I think its significant that no life that isn't carbon-based has been found on earth. If, say, silicon-based life were possible there's no reason that it couldn't have arisen here.

Maybe it did but got out-competed by the carbon-based rivals.

[Primula Baggins]

There's more to the question of life on other planets than satisfying our curiosity. Imagine being able to study how other forms of life, forming in an entirely separate environment, solved the same problems life on Earth faced. The results could have huge implications. Just the existence of life another world has huge implications, philosophical as well as scientific, even if it's just bacteria, or fossil bacteria as might be the case on Mars. (And I'm willing to bet we'll find a lot more than bacteria around those warm undersea vents on Europa.)

As much as I like knowing more about the cosmos, I'm leaning to the position that the high costs of space exploration mean we should approach it with caution. Everyone is thrilled by the Curiosity rover, for example, but $2.5 billion dollars seems like a hell of a lot to me to bring back some (in my view) pretty unclear pictures of Mars. A world that we already know enough about to know that it doesn't have all that much to offer us any time in the foreseable future. And with the economic situation as it is now, and as it is likely to continue, the idea of manned Mars exploration strikes me as insane.

I don't think that we should stop sending these probes. The New Horizons mission to Pluto, for example, will bring us images that we've never seen before. But it may be that Europa is a dead world with ice running straight down to rock and the proposed undersea oceans nothing but science fiction.

At risk of heresy, I see space exploration in the same terms as building sports stadiums. Certainly a justifiable use of public money but hardly a priority.

It boggles me that a sports stadium should be considered an equivalent good to better understanding the universe we live in. I know you say we should continue to explore, which I think means you understand where I'm arguing from; but others don't.

Why are theoretical or flatly unneeded weapons systems, or ridiculous public architecture boondoggles, or subsidies for dinosaur industries considered sensible investments, whereas exploring our universe and learning new things about the ultimate source of reality and our existence is not?

Where would we be as a civilization if no resources, no human effort had ever been expended on anything but safely profitable ventures?

It would still be 1443.

But I kind of like living in 2012.

[Túrin Turambar]

There does come a point, though, where the return on investment falls sharply. It is one thing to do the type of research that Copernicus, Galileo, Newton and Darwin et al did. It is another to spend literally billions to find out the exact composition of the atmosphere of Mars. I’d love to know what lies under the ice on Europa as well, but I really can’t see any spin-off that knowing that would lead, directly or indirectly, to an improved standard of living to humans on earth. That is the difference between that the types of science that pulled us out of the dark ages.

[River]

Well, back in the day, they thought that type of science was so bloody useless they forced Galileo to recant and he spent the rest of his life under house arrest. Some things only attain value in hindsight.

Drilling into the ice layer of Europa is arguably an extension of the work begun by the likes of the men you listed. They plucked the low-hanging fruit and we have feasted mightily. Getting more off that tree is not going to be easy.

[Frelga]

Yesterday, I learned that we owe LASIC surgery to technologies developed for space exploration.

Besides, it's not like they launched $2.5 billion to Mars. The money was paid here on Earth - here in the US, since I assume that like other Federal projects, it was required to use only domestically manufactured products. At a time when the US increasingly becomes a service economy while other countries take lead in new technologies such as solar energy, I'd say it's a pretty good place to invest.

Here's a (rather opinionated, but I didn't have time to google for more) article that argues the same thing:

Curiosity Comes Cheap - Why the latest Mars rover (and all planetary exploration) is a steal
Posted By Casey Dreier

No, NASA spread the cost of this mission out over eight years. The money spent went into salaries of highly-skilled engineers, programmers, managers, and independent contractors in over twenty states across the country. Things like the cost of rocket to launch it to Mars are included in that total, too, which accounts for nearly a fifth of the amount.

If you you just divide the total cost by the number of years NASA has saved for it, you come out with about $312 million per year. This works about to approximately 1.8% of NASA’s yearly budget and approximately diddly-squat of the total federal budget. That’s about $1 per year for every American, aka, nothing. Think of it this way: say you lose one dime every month this year. Whoops! You’ve lost more money than you spent on Curiosity.

[Primula Baggins]

I am probably weird (I know I'm a geek), but my standard of living would be immeasurably worse if I thought the human race no longer cared to expend any effort to find out what we don't know because we don't know it. Especially given how little the effort costs compared to what we spend giving lots of money to people who already have plenty, or blowing things up for no discernible reason, or building weapons that will never be used, or subsidizing industries that are harming the planet.