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So my buddy The Nazz, aka Nazzy aka @Shojarius aka Lord Nazzleby of Nightwatch-upon-Sweatshirt gave me a great, informative reply when I asked him the following question on YouTwitFace about the new world-shattering bacteria NASA announced:
Short Short Version: I’m not too surprised. And no, no arsenic in the lipid bilayer. 🙂
Short Version: I’m not too surprised. But there are reasons why some may be surprised. Legitimate reasons, too. It’s just that, I think that anyone with half a gram of open-mindedness would dismiss those concerns in the context of exobiology.
Long version: As you know, arsenic and phosphorus belong to the same periodic family (column) of elements. That is to say, electrochemically they ought to behave similarly to one another. They ought to both be somewhat electrophilic. They ought to both be seen forming structures like PO4 3minus (check) and AsO4 3minus (check). Etc, etc. But as you also know, there are some differences between the two elements, otherwise they wouldn’t be different elements (duh-hurrrr, Ryan is Captain Tautology), and these differences account for their different profiles in most living systems.
Part 1 – Size Phosphorus is “the right size” for forming DNA. This is because DNA (as we know it) is already made up of the other elements H, C, O, N, and S. On the whole, these are small elements. Only sulfur is anywhere near phosphorus’s size. So we expect phosphorus to be “pushing the envelope”, just a tad, as far as the size party goes. Arsenic, while only just slightly larger from a periodic table perspective (1 row down), is significantly larger from a biological perspective. Where phosphorus makes a snug fit, arsenic is much too big to fit into the proverbial hole. It doesn’t matter that he “behaves similarly” to phosphorus — if he can’t fit in the hole, and if he’s got to fit in the hole in order to fulfill a role fulfilled by phosphorus, then he’s clearly not similar enough to phosphorus.
Turf can probably tell you about this, being a medical student himself, but remember the molecule ATP that crops up everywhere in cell biology? It turns out that ATP actually doesn’t/”can’t” exist in vivo without the presence of magnesium ion, Mg2+. If you were to take all the magnesium in the body, (making up numbers here) 90% of it would be magnesium that migrates alongside ATP in the cell soup and only 10% of it would be magnesium in all other molecular structures. Magnesium’s job = ATP chaperone. Period. Well, funny thing is: we know that beryllium (rare, one size smaller) can’t substitute in for him, and neither can calcium (über-common, one size larger). Magnesium is the “perfect fit” that gets the job done.
I tell this story because it helps you to understand why some biologists may have ruled arsenic out from the start, just based on size alone. They look at the story of magnesium and they say, “Look, pals: wrong size, wrong profile. Simple as that. Quit wastin’ my time.” But there’s more. MUCH more.
Part 2 – Chelation
http://en.wikipedia.org/wiki/Chelation
You may ask, “Why is arsenic toxic but phosphorus isn’t?” And it has a surprisingly concise answer: chelation, chelation, chelation. Phosphorus is a poor chelator while arsenic is a magnificent chelator. Time for some fun WW1 history:
Chelation can (from a cell biological POV) be best seen as “throwing a wrench in the works,” quite literally. Arsenic goes into various molecular machines, be they mitochondrial or nuclear, and “gunks up” the machinery by forming inappropriate bonds. This is why arsenic is poisonous, and this is why scientists would typically not expect arsenic to be compatible with life — at least, not to the extent required by a bacterium to completely substitute arsenic for phosphorus in assembling DNA. There is natural arsenic in everyone’s bodies, but nowhere near the levels where substitution would be expected. It was thought that, if a cell had enough arsenic that it could assemble a DNA backbone made of the stuff, then it’d also logically have to have enough arsenic to completely shut down ~50% of the machinery inside the cell. Insta-death.
So, why am I not as surprised as some of the scientists? For one thing, I put a lot more stock in arsenic’s similarities to phosphorus than I think most of these experts did prior to their findings. Chemistry is a wonderful field, and if there’s one thing I’ve learned from it, it’s that almost every single element is a double-agent. Almost every element has the capacity to surprise you, to either act in one way or to act in one completely different way. So while I know of and appreciate the knowledge that arsenic is a magnificent chelator in living systems, I *also* can appreciate the possibility that, under the right circumstances, arsenic’s chelation tendencies might be tamed and it might be able to sit at the dinner table with the rest of the atomic family and behave.
But for a second thing, I’m not surprised because bacteria are remarkably versatile and, if the need presented itself, it would not surprise me that they could solve the problem of arsenic’s poisonous tendencies in any number of ways:
I mean, yeah, I’m REALLY simplifying matters, and I probably should be a lot more surprised than I am, but …
I dunno. I heard the news report the other day and all I could think over and over was: Tholians. http://en.wikipedia.org/wiki/Tholian (It’s not printed anywhere on the site, but my memory of Tholians is mostly from the PC game Klingon Academy, where I could swear it was stated in the manual or else in-game that they were silicon-based life forms.)
In my view, the most important thing in chemistry is bond formation. Bond formation is king. So so long as you can build the same structures dimensionally, I don’t care what size or color your building blocks had to be to pull it off. Your house may be 100x bigger than his house, but if he used carbons and you used silicons, then that’s okay. Do what you gotta do. It’s like the kid who builds a house out of Legos versus the kid who builds the exact same house but out of the Lego knockoffs you find in daycares that are like 100x the size of a normal Lego.
Of course, my question for @Shojarius (since I’ve decided he’s the expert) is…does the bacteria has an arsenolipid bilayer? A grand phraseHakeem the Dream Onazzawan’s answer is below:
Short Short Version: I’m not too surprised. And no, no arsenic in the lipid bilayer. 🙂
Short Version: I’m not too surprised. But there are reasons why some may be surprised. Legitimate reasons, too. It’s just that, I think that anyone with half a gram of open-mindedness would dismiss those concerns in the context of exobiology.
Long version: As you know, arsenic and phosphorus belong to the same periodic family (column) of elements. That is to say, electrochemically they ought to behave similarly to one another. They ought to both be somewhat electrophilic. They ought to both be seen forming structures like PO4 3minus (check) and AsO4 3minus (check). Etc, etc. But as you also know, there are some differences between the two elements, otherwise they wouldn’t be different elements (duh-hurrrr, Ryan is Captain Tautology), and these differences account for their different profiles in most living systems.
Part 1 – Size Phosphorus is “the right size” for forming DNA. This is because DNA (as we know it) is already made up of the other elements H, C, O, N, and S. On the whole, these are small elements. Only sulfur is anywhere near phosphorus’s size. So we expect phosphorus to be “pushing the envelope”, just a tad, as far as the size party goes. Arsenic, while only just slightly larger from a periodic table perspective (1 row down), is significantly larger from a biological perspective. Where phosphorus makes a snug fit, arsenic is much too big to fit into the proverbial hole. It doesn’t matter that he “behaves similarly” to phosphorus — if he can’t fit in the hole, and if he’s got to fit in the hole in order to fulfill a role fulfilled by phosphorus, then he’s clearly not similar enough to phosphorus.
Turf can probably tell you about this, being a medical student himself, but remember the molecule ATP that crops up everywhere in cell biology? It turns out that ATP actually doesn’t/”can’t” exist in vivo without the presence of magnesium ion, Mg2+. If you were to take all the magnesium in the body, (making up numbers here) 90% of it would be magnesium that migrates alongside ATP in the cell soup and only 10% of it would be magnesium in all other molecular structures. Magnesium’s job = ATP chaperone. Period. Well, funny thing is: we know that beryllium (rare, one size smaller) can’t substitute in for him, and neither can calcium (über-common, one size larger). Magnesium is the “perfect fit” that gets the job done.
I tell this story because it helps you to understand why some biologists may have ruled arsenic out from the start, just based on size alone. They look at the story of magnesium and they say, “Look, pals: wrong size, wrong profile. Simple as that. Quit wastin’ my time.” But there’s more. MUCH more.
Part 2 – Chelation
http://en.wikipedia.org/wiki/Chelation
You may ask, “Why is arsenic toxic but phosphorus isn’t?” And it has a surprisingly concise answer: chelation, chelation, chelation. Phosphorus is a poor chelator while arsenic is a magnificent chelator. Time for some fun WW1 history:
“Chelating agents were introduced into medicine as a result of the use of poison gas in World War I. The first widely used chelating agent, the organic dithiol compound dimercaprol (also named British Anti-Lewisite or BAL), was used as an antidote to the arsenic-based poison gas, Lewisite”http://en.wikipedia.org/wiki/Lewisite
Chelation can (from a cell biological POV) be best seen as “throwing a wrench in the works,” quite literally. Arsenic goes into various molecular machines, be they mitochondrial or nuclear, and “gunks up” the machinery by forming inappropriate bonds. This is why arsenic is poisonous, and this is why scientists would typically not expect arsenic to be compatible with life — at least, not to the extent required by a bacterium to completely substitute arsenic for phosphorus in assembling DNA. There is natural arsenic in everyone’s bodies, but nowhere near the levels where substitution would be expected. It was thought that, if a cell had enough arsenic that it could assemble a DNA backbone made of the stuff, then it’d also logically have to have enough arsenic to completely shut down ~50% of the machinery inside the cell. Insta-death.
So, why am I not as surprised as some of the scientists? For one thing, I put a lot more stock in arsenic’s similarities to phosphorus than I think most of these experts did prior to their findings. Chemistry is a wonderful field, and if there’s one thing I’ve learned from it, it’s that almost every single element is a double-agent. Almost every element has the capacity to surprise you, to either act in one way or to act in one completely different way. So while I know of and appreciate the knowledge that arsenic is a magnificent chelator in living systems, I *also* can appreciate the possibility that, under the right circumstances, arsenic’s chelation tendencies might be tamed and it might be able to sit at the dinner table with the rest of the atomic family and behave.
But for a second thing, I’m not surprised because bacteria are remarkably versatile and, if the need presented itself, it would not surprise me that they could solve the problem of arsenic’s poisonous tendencies in any number of ways:
- adopt a genome whose machinery is almost entire un-gunk-up-able
- keep the same genome, but run the assembly line non-effing-stop and keep pumping out replacement parts for the machines which free-floating arsenic keeps mucking up
- let someone else do all the work (e.g. if arsenic gunks up a machine which squirts water out of bacteria, then by taking up residence in a frighteningly salty environment, the bacteria won’t have to worry anymore about water freely migrating into him and therefore he won’t have to worry about the water pump being broken)
I mean, yeah, I’m REALLY simplifying matters, and I probably should be a lot more surprised than I am, but …
I dunno. I heard the news report the other day and all I could think over and over was: Tholians. http://en.wikipedia.org/wiki/Tholian (It’s not printed anywhere on the site, but my memory of Tholians is mostly from the PC game Klingon Academy, where I could swear it was stated in the manual or else in-game that they were silicon-based life forms.)
In my view, the most important thing in chemistry is bond formation. Bond formation is king. So so long as you can build the same structures dimensionally, I don’t care what size or color your building blocks had to be to pull it off. Your house may be 100x bigger than his house, but if he used carbons and you used silicons, then that’s okay. Do what you gotta do. It’s like the kid who builds a house out of Legos versus the kid who builds the exact same house but out of the Lego knockoffs you find in daycares that are like 100x the size of a normal Lego.
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