Methylation happens to the bases, not the backbone.
Yeah I know, but perhaps that stabilises the DNA anyway?
Bacteria don't have histones.
Yes, but Archae do. They are SCOP family 47129. Admittedly I didn't check to see if these organisms are Archae
Of course the enzymes are different; the enzymes in every individual in a population are slightly different, let alone the difference between the enzymes in different species. If this species has evolved a way to substitute arsenate for phosphate, then a whole lot of enzymes have probably changed to accommodate that change.
See this is where your list of 'corrections' start to unravel. Are they different folds? Different SNIPS? Different quaternary structure? What I was talking about was different _mechanisms_. Perhaps they use the same mechanisms but a slightly different blend of sidechains. Or perhaps the mechanisms themselves are different.
Life on earth is more diverse than your pedantic biology teacher taught you; this is an interesting example but hardly shocking news to real biologists.
Your condescending tone is misdirected. I'm well aware of life's diversity, having spent a decade or more studying it. I can't now remember if my biology teacher was pedantic or not, but I've read enough since then about metallozymes, ribozymes, extremophiles, phylogenetic empires, etc to make up for it.
the cell has either found a way to strengthen the backbone or has developed an amazing repair mechanism which can deal with frequent DNA damage
Hmmm. Maybe it methylates the DNA more? Or the histones are different. I guess - as you say - more repair enzymes is quite likely, since that just requires some promoter mutations.
The interesting question for me is whether any of the mechanisms are different for this organisms enzymes. For the last few months I've been sitting on the next desk to the maintainer of a database of biochemical mechanisms (MACiE - hi gemma, assuming you read slashdot, and happy birthday...) so maybe that's why it occurs to me. Many enzymes use ATP/NAD/other phosphate cofactors to make stuff, so if AsO4 has a slightly different chemistry, I wonder if different sidechains are used. Or, as I say, some completely different mechanisms (or pathways?).
evidence of exotic Earth-based life is NOT the same as evidence of extra-terrestrial life...
I am quite sure they are aware of that. However, the broader the range of environments in which we find life here, the broader the range of environments in which we might find life out there. I mean, it's far easier to look for something when you know the characteristics of what you're looking for.
Researchers may be aware of that, but there is always the implication that if you find an organism that can tolerate an environment different from Earth-normal this means planets out there with that environment could also support life. This doesn't follow at all - it might be that you need the more benign conditions found on most of the Earth in order to support enough life that some of that life can branch out into specialised areas like extreme salt, temperature, acidity, etc. In fact I strongly suspect this is the case.
I suppose the only way I can see extremophiles (such as this arsenate tolerant species) providing evidence for a broader range of planetary niches is for planets like Venus, which might once have been Earth-like, but have gone 'bad'. Some life might cling on in these circumstances, but not be able to provide a proper biosphere.
Oh, right. An arsenate DNA backbone. Makes sense, I suppose. Not as exotic as PNA (peptide nucleic acid) though, and that's been synthesised. I don't really see this as hugely exciting - interesting, yes, but not the same as some radically different architecture for organisms.
Silicon-based life : not possible, it doesn't form a diverse enough range of compounds.
Foreign DNA - low sequence identity with highly conserved proteins (histones, for example) would be odd. I doubt that is the case here.
ATCG - there is really only one way for these bases to form DNA. Well, there's A, B, and Z forms, and telomeres, but no new ways.
Different transcription/translation; possible, but again doubtful. Might have different tRNAs, I guess, if there are some special requirements for arsenate-amino acids.
Phosphate/arsenate switch - most likely scenario.
As a final note to researchers on 'terrestrial astrobiology' - evidence of exotic Earth-based life is NOT the same as evidence of extra-terrestrial life...
Perhaps its proteins use selenocysteines? Or it produces lots of de-arsenating enzymes, like bacteria that live in very hot temperatures (100 deg, say) produce more HSPs.
Or even Minecraft (or other sandbox games) where there essentially is no ending. I think playing it has taught me some things about setting reasonable goals when there are an infinity of possible tasks to do, with no real way of 'completing' those tasks. I mean, sure I can finish trying to mine some diamond, or make a portal, or a bridge - but there are always more diamonds to be mined...
Sometimes you just come up against some blatently unfair or extremely hard section of the game and give up.
Dara Ó Briain calls this effect "games deny[ing] you content", and talks about GTA (where he claims never to have seen Manhattan because of the dullness of driving in traffix), and Gears of War (where the bit where you have to dodge through doorways he's never done):
http://www.youtube.com/watch?v=eG3aHvPG6H8
Indeed. There was a story in the UK papers about a 3yr old child injured by a flying Chinese lantern. He was underneath it, making a wish, and got facial injuries from hot wax.
The father's comment was (paraphrased) : "Why are they selling things which are dangerous? They should make them safe, or ban them". Which makes a superficial kind of sense, but surely nothing is safe in all circumstances. We all laugh at labels on products that say "Don't stand underneath this hot, flying candle", but perhaps people could occasionally try keeping themselves safe, rather than relying on others to do so.
Thanks for the support on logic fallacies, it isn't even amusing anymore when people throw in labels they've read in another thread instead of arguments
No problem. It annoys me as well. Especially "ad hominem".
From what little biology I remember from school, the immunization that would result from mithridization would be precisely an acquired trait.
I could be wrong though.
Ah, well it is acquired for the individual, but not for its children. As wikipedia says, drinking alcohol is a good example - the more you drink, the more of the detoxification machinery is made by the body, so the more drinks it takes to get you drunk. Your children won't benefit from this immunity, however.
Agreed. Seems like a classic case of "This poster's opinion differs from mine, so he's offtopic". I also (partially) disagree with siddesu's take on this, but it is clearly ON topic.
I do have modpoints, but am resisting using them to point out two things.
Firstly, you are of course correct that without some understanding of the mechanism, any explanation based on Darwinian evolution is premature. For a start, it is a very short timescale, but who knows - we could speculate that some mutation in the active site of the enzyme that was targeted by this poison has rendered it ineffective.
Secondly, 'mithridization' refers to dosing yourself with small amounts of a poison until you build up an immunity. It has nothing to do with acquired characteristics (or epigenetics).
Oh, and yes it wasn't a straw man argument. SLASHDOTTERS: please do not use formal names for logical fallacies if you don't understand what they mean!
When you tweak one thing, something else tends to go out of balance. Still, this is pretty cool, whether it leads directly or indirectly to new treatments.
The best example of this, I think, is the theory of balance between cancer and auto-immune disease. The idea is based on the fact that cancer involves cells growing out of control, while auto-immune disease (like arthritis) involves the immune system attacking the self. So a more active immune system will lead to arthritis, and a less active one to cancer - and you can't just suppress or boost immune cell-killer response without consequence
Also, last time I checked both Germany, Japan and pretty much the rest of the planet used the metric system, so:
Yes, but slashdot is American, so it doesn't seem unreasonable that non-metric units creep in a lot of the time. It would be nice if there was automated translation of the units in articles, set by user preferences. So I (as a Brit) would see 600km...1000km....43 km/h...etc and US citizens (and Liberians, and Myanmar..er...ians) could choose the 100 miles...etc version.
I agree that all options should be considered (except, perhaps, doing nothing). However, 'adaptation' may not be as easy to do. Although it's a crude analysis, consider what would happen if everyone moved with the changes in temperatures. In other words, those in tropical areas moved to temperate ones, and temperate to tundra, as the world warmed.
It should be pretty obvious that there is a geometric problem here - you can only move so far north or south before someone starts running out of room. When alarmists make apocalyptic predictions, they are not usually talking just about the physics or warming, but also the human geography and politics. What happens if everyone wants to live in Iceland? Well, or Canada/Russia, which are a bit bigger:)
Of course, humans can adapt to their environment with technology - but I don't think turning up the air-con will be enough, somehow.
There are not going to be any underwater ruins. You are watching too many bad Kevin Costner movies.
Hey, hey. Say what you want about AGW, but don't run down 'Waterworld'! I watched it again the other day, and it's really a great-bad film; as in, enjoyably bad.
What other films have fights between catamarans and jetskis (which seem incredibly robust - they can hang around underwater for hours)? Or Dennis Hopper being fitted for a false eye by his sycophantic minions? Or races through a pirate oil tanker? Great stuff!
Although you are correct in the common use of 'Peak Oil', I find the common use is misleading as c6gunner pointed out by by his statement about the US also reaching peak-nuclear a few decades ago.
I agree that it is sometimes used (incorrectly) to mean, essentially "there is no more oil!!!1!". However, buggy whips and oil are not the really the same kind of thing - and 'nuclear' is not like either of them. Uranium might have a peak, I suppose, but that's a whole other discussion
Countries intentionally limit production (OPEC much?) to manipulate prices.
When it is known that 'Peak Oil' refers specifically to production but it is used to say 'the end is nigh, the US is evil' then it looks like, well, a Shell game.
Heh, was that a pun? Oddly enough, I have relatives who work for Shell. Doesn't mean I know anything about upstream of course; but maybe some of the jargon has rubbed off on me.
Hmmm. I'm a little confused by your assumption that everyone has their own personal definition of what "peak oil" means. I'm fairly certain that there is only one accepted meaning for the term, however useful or useless. I mean, I'm all for refining the usage of words and technical terminology - but not to the point of having individual relationships with words.
I don't find myself discussing peak oil very often, but if I wanted a term that meant "the point at which production starts to decline" then I think it would come in pretty useful....
Funny, I could have sworn that the US still has the worlds largest supply of oil shale. Plus oil sand. Plus coal. Plus plenty of offshore oil, and oil in Alaska. I guess "peak oil" to you just means "we have less than we used to"?
To most people, "peak oil" is the point at which production is at a peak. After this point, a country (or the world) is _producing_ less then they used to. Unless the oil shales have reversed the trend in the US, it does seem like that point has been reached.
"Had the bomb been armed with its fissile capsule" could be replaced with "had the bomb contained a black hole or killer vampire ghost" and be about as scary. it wasn't armed for exactly that kind of situation.
Wait, wait, wait....
So you're saying that the US has bombs with vampire ghost payloads now? AND black holes?!!
Slashdot Mirror
Methylation happens to the bases, not the backbone.
Yeah I know, but perhaps that stabilises the DNA anyway?
Bacteria don't have histones.
Yes, but Archae do. They are SCOP family 47129. Admittedly I didn't check to see if these organisms are Archae
Of course the enzymes are different; the enzymes in every individual in a population are slightly different, let alone the difference between the enzymes in different species. If this species has evolved a way to substitute arsenate for phosphate, then a whole lot of enzymes have probably changed to accommodate that change.
See this is where your list of 'corrections' start to unravel. Are they different folds? Different SNIPS? Different quaternary structure? What I was talking about was different _mechanisms_. Perhaps they use the same mechanisms but a slightly different blend of sidechains. Or perhaps the mechanisms themselves are different.
Life on earth is more diverse than your pedantic biology teacher taught you; this is an interesting example but hardly shocking news to real biologists.
Your condescending tone is misdirected. I'm well aware of life's diversity, having spent a decade or more studying it. I can't now remember if my biology teacher was pedantic or not, but I've read enough since then about metallozymes, ribozymes, extremophiles, phylogenetic empires, etc to make up for it.
the cell has either found a way to strengthen the backbone or has developed an amazing repair mechanism which can deal with frequent DNA damage
Hmmm. Maybe it methylates the DNA more? Or the histones are different. I guess - as you say - more repair enzymes is quite likely, since that just requires some promoter mutations.
The interesting question for me is whether any of the mechanisms are different for this organisms enzymes. For the last few months I've been sitting on the next desk to the maintainer of a database of biochemical mechanisms (MACiE - hi gemma, assuming you read slashdot, and happy birthday...) so maybe that's why it occurs to me. Many enzymes use ATP/NAD/other phosphate cofactors to make stuff, so if AsO4 has a slightly different chemistry, I wonder if different sidechains are used. Or, as I say, some completely different mechanisms (or pathways?).
evidence of exotic Earth-based life is NOT the same as evidence of extra-terrestrial life...
I am quite sure they are aware of that. However, the broader the range of environments in which we find life here, the broader the range of environments in which we might find life out there. I mean, it's far easier to look for something when you know the characteristics of what you're looking for.
Researchers may be aware of that, but there is always the implication that if you find an organism that can tolerate an environment different from Earth-normal this means planets out there with that environment could also support life. This doesn't follow at all - it might be that you need the more benign conditions found on most of the Earth in order to support enough life that some of that life can branch out into specialised areas like extreme salt, temperature, acidity, etc. In fact I strongly suspect this is the case.
I suppose the only way I can see extremophiles (such as this arsenate tolerant species) providing evidence for a broader range of planetary niches is for planets like Venus, which might once have been Earth-like, but have gone 'bad'. Some life might cling on in these circumstances, but not be able to provide a proper biosphere.
Oh, right. An arsenate DNA backbone. Makes sense, I suppose. Not as exotic as PNA (peptide nucleic acid) though, and that's been synthesised. I don't really see this as hugely exciting - interesting, yes, but not the same as some radically different architecture for organisms.
As a final note to researchers on 'terrestrial astrobiology' - evidence of exotic Earth-based life is NOT the same as evidence of extra-terrestrial life...
Perhaps its proteins use selenocysteines? Or it produces lots of de-arsenating enzymes, like bacteria that live in very hot temperatures (100 deg, say) produce more HSPs.
for an announcement this big they would have to have found adenosine triadenide.
Adenosine Triarsenate? (ATA)
He said the word of god. Not the word "god".
reading comprehension: try it some time
No, the OP really did put "the word god". Perhaps they _meant_ "the word of God" (or "the word 'God'..."), but that's not what was typed.
Or even Minecraft (or other sandbox games) where there essentially is no ending. I think playing it has taught me some things about setting reasonable goals when there are an infinity of possible tasks to do, with no real way of 'completing' those tasks. I mean, sure I can finish trying to mine some diamond, or make a portal, or a bridge - but there are always more diamonds to be mined...
Sometimes you just come up against some blatently unfair or extremely hard section of the game and give up.
Dara Ó Briain calls this effect "games deny[ing] you content", and talks about GTA (where he claims never to have seen Manhattan because of the dullness of driving in traffix), and Gears of War (where the bit where you have to dodge through doorways he's never done): http://www.youtube.com/watch?v=eG3aHvPG6H8
Indeed. There was a story in the UK papers about a 3yr old child injured by a flying Chinese lantern. He was underneath it, making a wish, and got facial injuries from hot wax.
The father's comment was (paraphrased) : "Why are they selling things which are dangerous? They should make them safe, or ban them". Which makes a superficial kind of sense, but surely nothing is safe in all circumstances. We all laugh at labels on products that say "Don't stand underneath this hot, flying candle", but perhaps people could occasionally try keeping themselves safe, rather than relying on others to do so.
Thanks for the support on logic fallacies, it isn't even amusing anymore when people throw in labels they've read in another thread instead of arguments
No problem. It annoys me as well. Especially "ad hominem".
From what little biology I remember from school, the immunization that would result from mithridization would be precisely an acquired trait.
I could be wrong though.
Ah, well it is acquired for the individual, but not for its children. As wikipedia says, drinking alcohol is a good example - the more you drink, the more of the detoxification machinery is made by the body, so the more drinks it takes to get you drunk. Your children won't benefit from this immunity, however.
Agreed. Seems like a classic case of "This poster's opinion differs from mine, so he's offtopic". I also (partially) disagree with siddesu's take on this, but it is clearly ON topic.
I do have modpoints, but am resisting using them to point out two things.
Firstly, you are of course correct that without some understanding of the mechanism, any explanation based on Darwinian evolution is premature. For a start, it is a very short timescale, but who knows - we could speculate that some mutation in the active site of the enzyme that was targeted by this poison has rendered it ineffective.
Secondly, 'mithridization' refers to dosing yourself with small amounts of a poison until you build up an immunity. It has nothing to do with acquired characteristics (or epigenetics).
Oh, and yes it wasn't a straw man argument. SLASHDOTTERS: please do not use formal names for logical fallacies if you don't understand what they mean!
When you tweak one thing, something else tends to go out of balance. Still, this is pretty cool, whether it leads directly or indirectly to new treatments.
The best example of this, I think, is the theory of balance between cancer and auto-immune disease. The idea is based on the fact that cancer involves cells growing out of control, while auto-immune disease (like arthritis) involves the immune system attacking the self. So a more active immune system will lead to arthritis, and a less active one to cancer - and you can't just suppress or boost immune cell-killer response without consequence
Also, last time I checked both Germany, Japan and pretty much the rest of the planet used the metric system, so:
Yes, but slashdot is American, so it doesn't seem unreasonable that non-metric units creep in a lot of the time. It would be nice if there was automated translation of the units in articles, set by user preferences. So I (as a Brit) would see 600km...1000km....43 km/h...etc and US citizens (and Liberians, and Myanmar..er...ians) could choose the 100 miles...etc version.
Maybe there is a firefox plugin for this?
How many times do people have to be told? SHE IS NOT A WITCH!!1!
She's you, she's nothing you've ever seen....
I agree that all options should be considered (except, perhaps, doing nothing). However, 'adaptation' may not be as easy to do. Although it's a crude analysis, consider what would happen if everyone moved with the changes in temperatures. In other words, those in tropical areas moved to temperate ones, and temperate to tundra, as the world warmed.
It should be pretty obvious that there is a geometric problem here - you can only move so far north or south before someone starts running out of room. When alarmists make apocalyptic predictions, they are not usually talking just about the physics or warming, but also the human geography and politics. What happens if everyone wants to live in Iceland? Well, or Canada/Russia, which are a bit bigger :)
Of course, humans can adapt to their environment with technology - but I don't think turning up the air-con will be enough, somehow.
There are not going to be any underwater ruins. You are watching too many bad Kevin Costner movies.
Hey, hey. Say what you want about AGW, but don't run down 'Waterworld'! I watched it again the other day, and it's really a great-bad film; as in, enjoyably bad.
What other films have fights between catamarans and jetskis (which seem incredibly robust - they can hang around underwater for hours)? Or Dennis Hopper being fitted for a false eye by his sycophantic minions? Or races through a pirate oil tanker? Great stuff!
I think he might be using the term 'most people' as an ironic understatement. That is the definition...
It's true, I was using understatement - perhaps because I'm British; I can't help it. :)
Although you are correct in the common use of 'Peak Oil', I find the common use is misleading as c6gunner pointed out by by his statement about the US also reaching peak-nuclear a few decades ago.
I agree that it is sometimes used (incorrectly) to mean, essentially "there is no more oil!!!1!". However, buggy whips and oil are not the really the same kind of thing - and 'nuclear' is not like either of them. Uranium might have a peak, I suppose, but that's a whole other discussion
Countries intentionally limit production (OPEC much?) to manipulate prices. When it is known that 'Peak Oil' refers specifically to production but it is used to say 'the end is nigh, the US is evil' then it looks like, well, a Shell game.
Heh, was that a pun? Oddly enough, I have relatives who work for Shell. Doesn't mean I know anything about upstream of course; but maybe some of the jargon has rubbed off on me.
Hmmm. I'm a little confused by your assumption that everyone has their own personal definition of what "peak oil" means. I'm fairly certain that there is only one accepted meaning for the term, however useful or useless. I mean, I'm all for refining the usage of words and technical terminology - but not to the point of having individual relationships with words.
I don't find myself discussing peak oil very often, but if I wanted a term that meant "the point at which production starts to decline" then I think it would come in pretty useful....
Funny, I could have sworn that the US still has the worlds largest supply of oil shale. Plus oil sand. Plus coal. Plus plenty of offshore oil, and oil in Alaska. I guess "peak oil" to you just means "we have less than we used to"?
To most people, "peak oil" is the point at which production is at a peak. After this point, a country (or the world) is _producing_ less then they used to. Unless the oil shales have reversed the trend in the US, it does seem like that point has been reached.
A relevant graph from wikipedia
And by falling apart I don't mean charts and graphs, I mean "The Day After Tomorrow" falling apart.
So, superstorms that freeze the Earth, and CGI wolves?
"Had the bomb been armed with its fissile capsule" could be replaced with "had the bomb contained a black hole or killer vampire ghost" and be about as scary. it wasn't armed for exactly that kind of situation.
Wait, wait, wait.... So you're saying that the US has bombs with vampire ghost payloads now? AND black holes?!!