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Anthony Salvagno
Preliminary Tobacco Seed Growth “Results”: Those are images of the first batch of samples (Dark Virginia seeds, ... http://t.co/aI1zhjD
"jump the shark now" ?? - Mickey Schafer
Yeah, I wondered about that. I think Anthony means something like "let the cat out of the bag". - Bill Hooker
Hey Bill, here's a response to you from the other thread: Hey Bill -- I've read a lot of those studies. Heavy water tends to stabilize biomolecules and biomolecular aggregates. Microtubules are very susceptible to this stabilization, and thus heavy water toxicity to eukaryotes resembles anti-mitotic drugs such as taxol that stabilize microtubules and prevent cell division. Lewis' hypothesis (and our working hypothesis) is not that D-depletion would be beneficial, but, rather, would be detrimental. It's also possible it is benefecial or has no effect, but most exciting would be if deuterium is used speicifically by some cellular processes. The concentration of deuterium in sea water is comparable to calcium and potassium (http://en.wikipedia.org/wiki...), both of which are essential. So, from that sense, it's not unreasonable that life would use deuterium. A caveat, though, is that deuterium spends most of it's time covalently bound to oxygen (in DOH molecules), so it's not really a free ion at that concentration. - Steve Koch
I think by "jump the shark" he meant I don't have any awesome idea to mention yet. I don't think there's a cat in the bag--a reliable metric is something he's searching for. - Steve Koch
Presumably [D+] depends on pH? Perhaps an organism adapted to low pH might be more susceptible -- or the effect of pH on any organism or system might be altered by D levels? - Bill Hooker
You can D-replace prokaryotes... what would happen if you did that for 100, or 100 million, generations, then switched 'em back to regular water? Can you H-replace 'em using D-depleted water? I'm trying to come up with ways to adapt some enzyme or other to D, wondering if you could get it sensitive enough that adding D to a system using that enzyme would act as a switch... - Bill Hooker
(P.S. have I mentioned how awesome this project is? Because it is seriously awesome. This is what I thought it would be like to be a scientist, when I was a kid and had no concept of grants and reviews and tenure and all that shit. Following this project in an Open notebook makes me feel like a kid again.) - Bill Hooker
yes pD (i.e. -log[D]) depends on pH, although that is an even bigger can of worms than I think I realized until now. Because D-O is a stronger bond than D-H, the pD of pure D2O is about 7.4 (see, e.g. http://www.madsci.org/posts...). So even though the ratio of D to H in "normal" water is 1/6600-ish, the ratio of free D to free H is even lower. However, why do we care about pH? Often because we want to know whether amino acid groups are charged or not, right? Well, those pka's must be different too, because D-N, D-O bonds are stronger. Sooooo, ummmmm.... I realize that I (and Anthony) have a lot to learn about this. Andy was aware of the first order problem--that you can't measure the pL (pL is the generic term for pH or pD that I have seen used, I think pL = -log (concentration of free H+D) with a pH meter, unless you adjust the reading. So, Andy adjusted the pH for his heavy buffer different from the normal buffer (see http://openwetware.org/wiki...). He set his heavy water buffers to a pL (pD) +0.41 from the pH of the normal buffer. At the time, we were following a reference which I think is http://pubs.acs.org/doi.... And...FUCK, I think Andy made a mistake and subtracted instead of added...FUCK. This sucks, but at least his dissertation is open so we can make a note if I am correct in noticing this now (very late unfortunately) - Steve Koch
Well, that big problem aside (I don't think it accounts for our results, since heavy-oxygen water also showed a gliding speed affect. I hope), I am still so confused that I am losing confidence that adjusting the "pL" that way is "correct." Furthermore, I am not even sure there is a "correct" way to do it, since H->D affects different bonds differently. I am thinking that for Anthony's work with living cells, we have to worry about this less, because organisms have mechanisms to adjust their own pH. Furthermore, for deuterium-depleted water, compared with normal water, the pL doesn't change much, since the D wasn't prevalent to begin with. I think I overstated importance of pH on Anthony's blog notebook yesterday. - Steve Koch
I love your idea about using acidophiles to amplify an effect of deuterium-depletion! (http://en.wikipedia.org/wiki...) Although I am too confused to know whether it would amplify or attenuate the affect. There must be plants that are acidophilic (I remember as a kid someone telling me that pine trees make the soil more acidic to fight off competitor plants...not sure if that is true). I would love a reason to study cactuses or archaea :) - Steve Koch
And thank you Bill for saying the project is awesome and for your encouragement and ideas since the start! I share your sentiment and feel like a kid scientist again too--whether we can do it and still get tenure (me) and money (us) remains to be seen, but I decided WTF, but probably wouldn't have pursued it without your interest. When we publish in PLoS ONE you should be a co-author if you want to. I wish you were in Albuquerque so Anthony could learn from you, I have a feeling (but don't actually know) that you've done some very careful experimentation in biomolecular science. - Steve Koch
Sorry, I'm late to the show, but all this notebooking has actually made me less accessible than I want to be. Also sorry for my improper use of jumping the shark. I meant it as you all interpreted it and not as it is actually defined. Oops! - Anthony Salvagno
Also thanks everyone for your great suggestions and comments! This project and my new notebook has raised my spirits to levels beyond my imagination. Like Bill and Steve stated I feel like a kid again too (even though I'm relatively young) and I get to report on really cool basic science that surprisingly hasn't been very deeply investigated. This project is literally like "I wonder what would happen if..." and then we get to see! Very exciting stuff. - Anthony Salvagno
Finally I just want to comment that I'm working on ways to improve my notebook and very much welcome any and all suggestions. - Anthony Salvagno