Sciencemadness Discussion Board

Carbon-silicon bonds

Morgan - 26-11-2016 at 08:42

http://www.sciencealert.com/for-the-first-time-living-cells-...
https://www.reddit.com/r/science/comments/5ex0qw/for_the_fir...

byko3y - 26-11-2016 at 09:10

Loud noise - nothing important happenned. Silane does not exists on the planet in a free form, neither does azide ester.
At common for the planet earth temperatures and in the presence of oxygen, silicon strongly prefers to form polymeric SiO2, which is really hard to break. Unlike carbon, sulfur, phosphorus, which are all widely incorporated into living cells. Phosphorus in its oxidized form though, because it's hard to reduce and is quickly oxidized by oxygen.

[Edited on 26-11-2016 by byko3y]

aga - 26-11-2016 at 11:52

Silane does exist on the planet, yet it is certainly not free - costs quite a lot for a cylinder of the stuff.

The main problem with silicon-based life is it's attitude to us carbonites.

The first Star Trek silicon-based lifeform referred to humans as "ugly bags of mostly-water".

wg48 - 26-11-2016 at 15:02

Quote: Originally posted by Morgan  
http://www.sciencealert.com/for-the-first-time-living-cells-...
https://www.reddit.com/r/science/comments/5ex0qw/for_the_fir...


Like many pop science articles the one above has some inaccuracies. It states that life does not using silicon which is incorrect.

Diatoms have been using silicon for their skeletons for about 100 million years. Many plants in particular grasses use silicon in their leaves. Rice husks are used as a source of silica. Silicon is considered a micronutrient for some plants.

I have about 4kg of biogenic silica its called diatomaceous earth.

Morgan - 26-11-2016 at 17:54

Quote: Originally posted by wg48  
Quote: Originally posted by Morgan  
http://www.sciencealert.com/for-the-first-time-living-cells-...
https://www.reddit.com/r/science/comments/5ex0qw/for_the_fir...


Like many pop science articles the one above has some inaccuracies. It states that life does not using silicon which is incorrect.

Diatoms have been using silicon for their skeletons for about 100 million years. Many plants in particular grasses use silicon in their leaves. Rice husks are used as a source of silica. Silicon is considered a micronutrient for some plants.

I have about 4kg of biogenic silica its called diatomaceous earth.


According to the article "No living organism is known to put silicon-carbon bonds together, even though silicon is so abundant, all around us, in rocks and all over the beach," says Jennifer Kan, a postdoctoral scholar in Arnold's lab and lead author of the new study.
I'm pretty sure they're aware of diatoms and horsetails and such. What they're talking about is the "unnatural bond".

Here's another version of the article from Caltech.
https://www.caltech.edu/news/bringing-silicon-life-53049

PHILOU Zrealone - 27-11-2016 at 11:57

Quote: Originally posted by byko3y  
Loud noise - nothing important happenned. Silane does not exists on the planet in a free form, neither does azide ester.
At common for the planet earth temperatures and in the presence of oxygen, silicon strongly prefers to form polymeric SiO2, which is really hard to break. Unlike carbon, sulfur, phosphorus, which are all widely incorporated into living cells. Phosphorus in its oxidized form though, because it's hard to reduce and is quickly oxidized by oxygen.

Really?

Organic silicium G5... found into urtica plant --> CH3-Si(OH)3

Useful for cartilage, skin elasticity, ...

NitratedKittens - 28-11-2016 at 04:05

Also not to mention that stinging nettles actually create glass needles on their surface.

Sulaiman - 28-11-2016 at 11:58

came across this whilst surfing and remembered this thread
http://cen.acs.org/articles/94/i47/Protein-provides-new-rout...

Morgan - 28-11-2016 at 13:39

The bacteria Arnold and Kan are using.
https://microbewiki.kenyon.edu/index.php/Rhodothermus_marinu...

Fulmen - 28-11-2016 at 15:05

Quote: Originally posted by PHILOU Zrealone  

Organic silicium G5... found into urtica plant --> CH3-Si(OH)3


Really? I can't find anything about this, as far as I can tell it's a synthetic supplement. And that plants utilize silica (as in silicium dioxide) is nothing new, ordinary grass contain lots of silica. But carbon-silicon bonds? Please show me a source for this.

Assuming their claims is right, biological carbon-silicon reactions has never been encountered in nature before. But is that true?
They started with a protein that "also happens to act like an enzyme to create silicon-carbon bonds at low levels". Assuming they didn't change the parameters significantly to get this action, it was already available in nature. Right?
Even if they did, they were able to produce an efficient enzyme in a few steps. Doesn't this suggest that nature was so close to such a pathway we can assume it must have been tried by nature before?

If carbon-silicon bonds were useful in biology, wouldn't nature have figured it out by now? Perhaps there are examples out there to be discovered? But even so, their lack of abundance suggests it's not a particularly useful pathway.

Everybody talks about how similar silicon is to carbon, but if that were true wouldn't we find silanes everywhere? But we don't. We can detect organics in interstellar clouds for christ's sake. Carbon chemistry is everywhere. Why mess with silicon when carbon is so much easier to work with?

Maroboduus - 28-11-2016 at 15:17

Quote: Originally posted by PHILOU Zrealone  
Quote: Originally posted by byko3y  
Loud noise - nothing important happenned. Silane does not exists on the planet in a free form, neither does azide ester.
At common for the planet earth temperatures and in the presence of oxygen, silicon strongly prefers to form polymeric SiO2, which is really hard to break. Unlike carbon, sulfur, phosphorus, which are all widely incorporated into living cells. Phosphorus in its oxidized form though, because it's hard to reduce and is quickly oxidized by oxygen.

Really?

Organic silicium G5... found into urtica plant --> CH3-Si(OH)3

Useful for cartilage, skin elasticity, ...


Useful mainly for ripping off those ignorant enough to believe in such snake oil remedies.

Morgan - 28-11-2016 at 18:36

Another presentation of the story, maybe a few crumbs different.
http://www.nature.com/news/living-cells-bind-silicon-and-car...

PHILOU Zrealone - 30-11-2016 at 10:21

I hardly imagine that diatom grows their silicium based frustule without organo-silicium linkage of some sort involved into the biosynthetic process.

NANOSTRUCTURE OF THE DIATOM FRUSTULE AS REVEALED BY ATOMIC FORCE AND SCANNING ELECTRON MICROSCOPY



[Edited on 30-11-2016 by PHILOU Zrealone]

mayko - 30-11-2016 at 11:02

I can't find a whole lot on the biochemistry of diatom silica formation, but it appears to take place through the polymerization of silicic acid upon an organic scaffold:
http://schaechter.asmblog.org/schaechter/2011/05/hard-biolog...

There might be some enzymatic activity involved in transporting and sequestering the monomer, but it's not obvious that C-Si covalent bonds are necessary for the process.

I've attached the original paper in case it clears any of this up.

Attachment: phpDfy115 (609kB)
This file has been downloaded 610 times

Morgan - 30-11-2016 at 11:05

Some background tidbits on diatoms
Evidence for a Regulatory Role of Diatom Silicon Transporters in Cellular Silicon Responses
"The sensing and transport of silicic acid are key aspects of understanding diatom silicon utilization. At low silicic acid concentrations (<30 μM), transport mainly occurs through silicic acid transport proteins (SITs), and at higher concentrations it occurs through diffusion."
"The average concentration of dissolved silicic acid [Si(OH)4, referred to here as Si] in the world's oceans is about 70 μM, but the Si concentration of surface water, which is the diatom habitat, is generally less than 10 μM and sometimes less than 1 μM (5, 9). An exception is the Southern Ocean, which has a silicic acid concentration of 65 μM, a concentration at which the uncharged Si(OH)4 molecule passively diffuses through diatom cell membranes>
http://ec.asm.org/content/14/1/29.full

Morgan - 30-11-2016 at 11:34

It seems apparent they acknowledge there are carbon-silicon bonds in nature, but tout that what they're doing is unique by enhancing it, albeit humble beginnings. Or making end products not found in nature.
https://www.youtube.com/watch?v=h_OTCQ_fxuc#t=1m30s

unionised - 30-11-2016 at 13:20

Quote: Originally posted by PHILOU Zrealone  
I hardly imagine that diatom grows their silicium based frustule without organo-silicium linkage of some sort involved into the biosynthetic process.

NANOSTRUCTURE OF THE DIATOM FRUSTULE AS REVEALED BY ATOMIC FORCE AND SCANNING ELECTRON MICROSCOPY

[Edited on 30-11-2016 by PHILOU Zrealone]


Reality has no reason to concern itself with what you imagine.

I can't see a reason why biology would bother to break the Si-O bond when it can just use the O as a handle to move the Si around with.

Fulmen - 30-11-2016 at 14:11

Quote: Originally posted by Morgan  
It seems apparent they acknowledge there are carbon-silicon bonds in nature

What they're saying is that some proteins can do this, not that it happens in nature. Could be that they're using chemicals or conditions that isn't found in any living organisms to achieve this.
Either way, nature is more than capable of producing C-Si bonds.

Morgan - 1-12-2016 at 05:52

So to be concise, some metallo-enzymes found in nature have some ability to catalyze carbon-silicon bonds, however "enzymes that catalyze carbon-silicon bond formation are unknown in nature."
http://science.sciencemag.org/content/354/6315/1048

"Cytochrome c from the bacterium Rhodothermus marinus, which is found in submarine hot springs in Iceland, catalyzed the reaction with 97% enantiomeric excess, although the catalytic turnover was still low."
http://cen.acs.org/articles/94/i47/Protein-provides-new-rout...

"Neither biological organosilicon compounds nor biosynthetic pathways to create them have been identified. But when given the right starting materials, some heme proteins can stereospecifically form carbon-silicon bonds..."
http://cen.acs.org/articles/94/i47/Protein-provides-new-rout...