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» The Geek Culture Forums!   » Techno-Talking   » Science!   » I've got crystals in my bacteria- and chocolate in my peanut butter! (Page 2)

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Author Topic: I've got crystals in my bacteria- and chocolate in my peanut butter!
Stibbons
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Icon 1 posted February 06, 2007 06:10      Profile for Stibbons   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by ScholasticSpastic:
Any idea, Stibbons, what the wee crystals might be made of? You can make a list if you like.

Nothing from me on this one, sorry. I'll ask some soily people when I get back in the dept...

quote:
And I would also not mind at all if you chose to dazzle us with your encyclopaedic knowledge of the history of dolomite (or whatever other rock catches your fancy).
Dolomite is a bit of an interesting rock, and it's existence poses a lot of questions. As I mentioned earlier, dolostone appears to be most abundant during greenhouse periods, times of high sea level, high atmospheric CO2, and low seawater carbonate saturation. Their petrography almost always suggests replacement of limestone (playing around with d13C and d18O, trace element concentrations such as Sr), and this is often backed up by evidence of volume changes in beds of dolostone.

Four mechanisms (aside from bacteria) are proposed for the formation of ancient dolomites. Mixing of sea (Mg rich) and meteoric (carbonate rich) waters could produce water with the right amount of the various chemicals required, but this operates only over a VERY small range of water mixes. A modern day example of this is in the Yucatan, but no dolomite is found there (aside from a small amount in ancient seds).

Seepage reflux (which sounds like a nasty medical condition [Smile] ) is where a lagoon fed by a seawater spring becomes hypersaline as the water evaporates. The saturation point of gypsum would be passed first, which would precipitate on the floor of the lagoon, increasing Mg/Ca. The resulting brine is denser than the incoming seawater, and would sink through the floor of the lagoon and back out to see. If the reflux occurs through l'stone there is potential for dolomitization due to the high [Mg]. A natural example is in the Antilles, where everything in this process occurs - except dolomitization.

Convection of seawater through volcanic atolls due to the high heat flow (yes, the volcano is long dead, but this is when the heat flow is highest - think how long heat would take to travel through the crust...) could induce convection currents through the overlying carbonates. As this would be seawater itself doing the replacement, the kinetic block stopping MgCa(CO3)2 being precipitated would have to be overcome, most likely by bacteria - again an example of this process occuring is the Bahama Banks, but little evidence of dolomitization is seen.

Finally, though not particularly important, are the "saddle" dolomites, which form at temperatures of 80-120C and are associated with Pb/Zn deposits, hydrocarbons, etc.

But despite all this, I've still no idea what your xtls are [Big Grin]

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ScholasticSpastic
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Icon 1 posted February 06, 2007 09:18      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
I likes geochemical stuff...

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

Posts: 540 | From: Vernal, UT | Registered: Jan 2007  |  IP: Logged
ScholasticSpastic
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Icon 1 posted February 11, 2007 23:29      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
Here's another image of the facultative anaerobes colonizing down into the media. I've managed to pull off much better contrast and color by playing with light sources. It looks kind of like an alien world seen from space. I guess, if one wanted to torture the metaphore, it is one.
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I've also played a bit with light sources to try to get better resolution on the crystals. Here are some examples:
 -  -
I've confirmed that there is definitely not a polarizer on the dissecting scope, but as soon as we get our sequence back I'm going to cut some plates open and extract crystals for finer examination under a real microscope. I'll try to verify the presence (or absence) of a polarizer on our other camera-equipped scope. Sure, I can see them fine without a camera, but then how will I show them off to you guys?
Here's another otherworldly one:
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And here's one more. It has some crystals in it, but I really like it for the contrasting shapes and colors of the colonies. What you're seeing is a contaminated plate, though, so its visual prettiness is undermined a little by its procedural ugliness...
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That's all for now. I probably won't be able to take pictures of the microfauna of my fish tank right away as next week is kind of full of tests for me and I should probably study a little.

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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SpazGirl
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Icon 1 posted February 12, 2007 08:10      Profile for SpazGirl   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
Man, I'm just stuck with enzymes right now, I miss culturing things. Virology is in two semesters though, which should prove to be really interesting [Smile]

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Things, and things.

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ScholasticSpastic
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Icon 1 posted February 12, 2007 09:21      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
I haven't had any classes where we get to do cultures yet. I found me a professor what needed an undergraduate research assistant. I'm excited to take micro next year- I'm, like, totally gonna ace that lab!

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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Ugh, MightyClub
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Icon 1 posted March 09, 2007 10:44      Profile for Ugh, MightyClub     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
ScholasticSpastic said:

I've confirmed that there is definitely not a polarizer on the dissecting scope, but as soon as we get our sequence back I'm going to cut some plates open and extract crystals for finer examination under a real microscope. I'll try to verify the presence (or absence) of a polarizer on our other camera-equipped scope. Sure, I can see them fine without a camera, but then how will I show them off to you guys?

Sorry to necropost, but Stibbons muttered something about a polarizer over here and that reminded me about this thread. Any news on the crystal front, Scholastic? I'm ready for more pics!

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Ugh!

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ScholasticSpastic
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Icon 1 posted March 09, 2007 11:27      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
I brought some mosses and alga from my tank to view under the microscopes, but I couldn't get the feed from the camera to work. I'm spending time with the manual to figure out where I've gone wrong. It looks like most of what lurks within the microfauna of my fishtank isn't particularly exciting, but there are quite a few species of benthic diatoms running around. Wanna see my diatoms? I'm not familiar with the acid-washing techniques to render bare silicate skeletons, but they look pretty neat with skin on, too. I'm also going to try to vary my sampling sites to see if I can find more micro-critters.

I'll have to take a look in the fridge and see if there are any plates we're ready to discard so I can cut out some crystals for a closer look. I'm excited to try that polarizer trick (the micro-microscope DOES have a polarizer- if I can get the camera to load to the computer).

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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Stibbons
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Icon 1 posted March 09, 2007 12:19      Profile for Stibbons   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by ScholasticSpastic:
[QB] Wanna see my diatoms? /QB]

Yeah! Give me some microfossil practice...
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ScholasticSpastic
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Icon 1 posted March 09, 2007 13:30      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
'Kay, I'll try to find some without the skin on for you.

--------------------
"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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ScholasticSpastic
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Icon 1 posted March 10, 2007 13:48      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
I've managed to cut out a crystal and take some pics at 100x magnification. The polarizer doesn't seem to have any effect on the crystals' appearance (oh, well).
 -  -  -  -
I'm actually a little let down- I was hoping for more coolness at high mag. It was difficult digging the crystal out of the plate. I had planned to take pics from several plates, but I had some samples from my fishtank with me and, well, those were easier to slap onto slides.
Starting a new thread for fishtank pics.

--------------------
"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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Tiroth
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Icon 11 posted May 23, 2007 15:17      Profile for Tiroth   Author's Homepage         Edit/Delete Post   Reply With Quote 
There is only one explanation. Bacteria are manufacturing and selling crystals so they can eventually buy out the strongest military countries on earth. Then, once they have done that, They will attack the lesser military powers one at a time. Bacteria will once more be the dominant organisms on Earth. We will be powerless.

-Tiroth

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Life is neither a good nor an evil; it is simply the place where good and evil exist.

-Seneca

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garlicguy

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Icon 1 posted May 23, 2007 16:01      Profile for garlicguy   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Tiroth:
There is only one explanation. Bacteria are manufacturing and selling crystals so they can eventually buy out the strongest military countries on earth. Then, once they have done that, They will attack the lesser military powers one at a time. Bacteria will once more be the dominant organisms on Earth. We will be powerless.

"And the meek shall inherit the Earth." Fine, fine, fine, Tiroth. But it is actually all about getting the chocolate and peanut butter together ala Reese's Peanut Butter Cups.

BTW - Why not intro yourself in an "All About You" thread, and tell us a bit about yourself?

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I don't know what I was thinking... it seemed like a good idea at the time.

Posts: 3753 | From: Pluto, no matter what you call it, is still my home. | Registered: Dec 2004  |  IP: Logged
Xanthine

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Icon 1 posted May 23, 2007 18:33      Profile for Xanthine     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Tiroth:
We will be powerless.

We sort of are already.

Mankind has been at war with germkind for as long as mankind has existed. We are not winning. We never were. We gained some ground with the advent of antibiotics, and some more with mass vaccination campaigns, but we are not winning. We have technology. They have numbers and rapid doubling times so they can out-evolve our technology as fast as we can develop it. In the long run, we be screwed.

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And it's one, two, three / On the wrong side of the lee / What were you meant for? / What were you meant for?
- The Decemberists

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Ashitaka

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Icon 1 posted May 24, 2007 04:25      Profile for Ashitaka     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Xanthine:
quote:
Originally posted by Tiroth:
We will be powerless.

We sort of are already.

Mankind has been at war with germkind for as long as mankind has existed. We are not winning. We never were. We gained some ground with the advent of antibiotics, and some more with mass vaccination campaigns, but we are not winning. We have technology. They have numbers and rapid doubling times so they can out-evolve our technology as fast as we can develop it. In the long run, we be screwed.

I disagree. Penicillin and the like failed because it does not kill bacteria, it weakens and then kills bacteria. Today, we are developing antibiotics that flat out kill bacteria instead of just weakening the cell wall, this way there is little chance for slightly mutated bacteria to survive and propagate. We will win.

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"If they're not gonna make a distinction between Muslims and violent extremists, then why should I take the time to distinguish between decent, fearful white people and racists?"

-Assif Mandvi

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Xanthine

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Icon 1 posted May 24, 2007 09:08      Profile for Xanthine     Send New Private Message       Edit/Delete Post   Reply With Quote 
I disagree with your disagreement. And my microbiology textbook backs me up. [Razz]

Penicillin attacks bacterial cell walls, causing the cells to break open (lyse, if you want to be polite/technical). The cells do not survive this process. However, there are bugs out there that carry an enzyme that breaks down penicillin and related drugs before penicillin can break the cell, and when penicillin is in the environment, those are the bugs that begin to dominate the population thanks to good old natural selection. They can do it pretty fscking quickly too - doubling times for bacteria vary from ~20 minutes to a day, depending on the species and what it's eating. There are some drugs that do simply stall out bacteria so your immune system can mop them up - I think tetracycline, kanamycin, and erythromycin are all bacteriostatic drugs. Most of the new antibiotics on the market are sexed-up variants on the older themes, mainly because we're running low on ways to hit bacteria without destroying our own cells. That said, new targets, and new weaknesses in the old targets, are being found. My thesis work involves two potential new drug targets, though designing the actual drug is going to be someone else's job. I'm just figuring out how the damn things work.

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And it's one, two, three / On the wrong side of the lee / What were you meant for? / What were you meant for?
- The Decemberists

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Ashitaka

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Icon 1 posted May 24, 2007 09:37      Profile for Ashitaka     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Xanthine:
I disagree with your disagreement. And my microbiology textbook backs me up. [Razz]

Penicillin attacks bacterial cell walls, causing the cells to break open (lyse, if you want to be polite/technical). The cells do not survive this process. However, there are bugs out there that carry an enzyme that breaks down penicillin and related drugs before penicillin can break the cell, and when penicillin is in the environment, those are the bugs that begin to dominate the population thanks to good old natural selection. They can do it pretty fscking quickly too - doubling times for bacteria vary from ~20 minutes to a day, depending on the species and what it's eating. There are some drugs that do simply stall out bacteria so your immune system can mop them up - I think tetracycline, kanamycin, and erythromycin are all bacteriostatic drugs. Most of the new antibiotics on the market are sexed-up variants on the older themes, mainly because we're running low on ways to hit bacteria without destroying our own cells. That said, new targets, and new weaknesses in the old targets, are being found. My thesis work involves two potential new drug targets, though designing the actual drug is going to be someone else's job. I'm just figuring out how the damn things work.

I work at a place whose sole purpose is to invent MSRA antibiotics. I know we are not out of ideas to kill these buggers. Developing drugs whose sole purpose is to bond with the enzymes that destroy your antibiotic and nullify its effect works wonders. ( I would really love to go into details and talk shop but I can't)((I don't invent these drugs either.)) I do analytical development.

I agree that no matter how you chose to kill the bacteria, natural selection could spare a few that could survive and become a new string. I believe with the new technologies we have now, we (the human race) will always be ahead of the curve, at least with antibiotics.

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"If they're not gonna make a distinction between Muslims and violent extremists, then why should I take the time to distinguish between decent, fearful white people and racists?"

-Assif Mandvi

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garlicguy

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Icon 1 posted May 24, 2007 16:35      Profile for garlicguy   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
For grins, try Preparation H. That'll fix the little mothers.

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I don't know what I was thinking... it seemed like a good idea at the time.

Posts: 3753 | From: Pluto, no matter what you call it, is still my home. | Registered: Dec 2004  |  IP: Logged


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