Wikipedia:Reference desk/Archives/Science/2010 October 7

= October 7 =

using sulfur to make carbon-carbon bonds
Are there any examples where for example, a sulfide attacks an electrophilic position to make some sort of cyclic intermediate or transition state, but then the intermediate/TS rearranges to eliminate the sulfur (maybe as an alkyl rearrangement). It doesn't necessarily have to leave the molecule, just make a new C-C bond.

i.e. RS- + R'X ---> R-S-R' + X-  ---> R-R'  [X is just an EWG, doesn't have to be halide or technically leave]

I see some interesting results from the Edman degradation reaction -- how does the sulfide leave the ring? Is this principle used in an any economically important drug syntheses?

Another route that I can see is to start from a sulfone and then make it possible for the sulfone to leave as sulfur dioxide.

I've not taken orgo III so I don't know the general principles of rearrangement reactions. They are rather mystifying to me. John Riemann Soong (talk) 00:23, 7 October 2010 (UTC)


 * One of the most common internal rearrangement reactions occurs in carbocation formation, such as you would find in an SN1 or E1 mechanism. See Rearrangement reaction for a general overview of different types of common rearrangements.  There's lots of blue links to follow for additional details.  Also, forming carbon-carbon bonds is often done via Organometallic chemistry which results in the formation of a carboanion.  The key in forming carbon-carbon bonds is making the carbon a nucleophile.  Common ways of achieving this are via Grignard reagents, Organolithium reagent, etc.  The carbon-sulfur bond is fairly non-polar, and things like sulfone result in carbocations (electrophilic) (assuming SN1-type leaving groups).  In fact, thiols make FANTASTIC leaving groups, so the positive part of the reaction can be a thiol.  However, you'd still need a good nucleophilic source of carbon, and you are pretty much back to organometallics there.  -- Jayron  32  01:40, 7 October 2010 (UTC)


 * There are no organometallics in the Edman degradation! I'm aiming for slightly milder conditions than superbases like Grignards and organolithiums. Do sulfones not interconvert into the tautomeric equivalents of enols?
 * Also, something with a small number of steps (I believe organometallic reactions are frequently tedious?) and an "elegant" rearrangement (to me, the Edman degradation is "elegant") I guess is what I had in mind. What is the general principle in the final rearrangement in the Edman degradation? John Riemann Soong (talk) 01:50, 7 October 2010 (UTC)
 * Sulfones can be deprotonated at the adjacent carbon (pKa ~ 30), but typically amine-bases like LDA or more commonly n-BuLi are used. It's not quite the same effect as an enolate because a sulfone isn't exactly an S=O bonding like a carbonyl C=O. You can deprotonate α to a sulfoxide, 5ish pKa units less acidic, and even at a position α to two thiols (not oxidized) in the same range as those two--definitely no resonance in that case. You can sure think of it that way and use the analogy to explain this sort of reaction though. DMacks (talk) 02:07, 7 October 2010 (UTC)
 * Ramberg–Bäcklund reaction. DMacks (talk) 01:51, 7 October 2010 (UTC)
 * Thanks! What is the usual pka of the C-H bond alpha to a sulfone? Can this pKa be lowered with an alternative choice of solvent to water (or a Lewis acid)? Do you really need a superbase to deprotonate it? John Riemann Soong (talk) 02:11, 7 October 2010 (UTC)
 * Those pKa are from DMSO...would be hard to measure such high pKa in water I assume. As with anything pKa, changing "what else" is attached to the position being deprotonated can have a large effect--here again enolates are a good comparison for a similar pattern. You can also change the electronegativity of the "other side" of the anion-stabilizing group. Here's some approximate pKa values (in DMSO) for the α-CH in various structures:


 * You can also add electron-withdrawing groups to the Ph, but probably only gives you a decrease of 2–3 pKa units.DMacks (talk) 18:12, 7 October 2010 (UTC)
 * The Eschenmoser sulfide contraction is also a reaction that's similar to that which you're talking about. Physchim62 (talk) 12:07, 7 October 2010 (UTC)
 * It doesn't seem as popular as it should for its utility. I mean the reagents look cheaper than a lot of expensive organometallics. John Riemann Soong (talk) 16:10, 7 October 2010 (UTC)

3-second Pop Tarts?
On my box of Pop Tarts, it says "Microwave on high setting for 3 seconds". But if I microwave them for such a short time, it has hardly any effect, and the Pop Tarts remain cold. I've seen many other people comment on this online, and I know that there's nothing wrong with my microwave. So why is there such a blatantly wrong instruction on the box? Were they sued by someone whose Pop Tarts burst into flame after 5 seconds? --140.232.178.74 (talk) 01:05, 7 October 2010 (UTC)
 * Presumably, that's so the Kellogs corporation ends up on the safe side of this: . Admitedly, this is a toaster, and not a microwave, but I still wouldn't want to end up on the wrong side of that.  -- Jayron  32  01:18, 7 October 2010 (UTC)


 * They are covering themselves. Sugary fillings go "nuclear" in microwaves very quickly, and will burn you pretty badly.217.158.236.14 (talk)

...sulfuric acid costs 9.8 cents a litre
(Average rate, from dividing 8 billion dollars by 165 million tonnes and factoring in the density of H2SO4.) I know there's economy of scale and all, especially when it comes to safe delivery....but why then does it cost a 100 bucks to order a 2.5L bottle of 95% sulfuric acid from Sigma-Aldrich? That's about 400 times more expensive. John Riemann Soong (talk) 01:10, 7 October 2010 (UTC)


 * So, do you have your own Winchester bottle you are going to drive up to your local sulfuric acid manufacturer, and ask them to top off for you? It isn't like the local dairy farm, where you can get your milk from the source on the cheap, and you don't really buy the stuff wholesale, unless you are buying a LOT of it.  The cost/liter is the cost of production, and does not factor in the costs associated with the transport, containment, and distribution of the substance.  The same sorts of cost inflation occurs for every product made on an industrial scale.  While the price you pay is often several hundred times more than the cost of the materials to make a product, it isn't like the company makes up the difference in pure profit.  There are LOTS of people to pay along the way.  -- Jayron  32  01:24, 7 October 2010 (UTC)


 * I just didn't expect the ratio to be so high. I'm sure the ratio for industrial meat (which has mega food safety concerns) versus consumer/supermarket meat doesn't exceed an order of magnitude very often... John Riemann Soong (talk) 01:34, 7 October 2010 (UTC)


 * It isn't just safety that drives up cost. Its how many hands are in the pie that does.  You have to pay all the people between you and the factory that makes the sulfuric acid, that means all the employees of those companies, including the receptionists and the accounants and the janitors and everyone else takes a cut along the way, in every single company.  The chain involved in getting a T-bone steak to your table is actually a lot shorter, since the grocery store you buy it from probably gets it straight from the slaughterhouse.  -- Jayron  32  01:43, 7 October 2010 (UTC)
 * Here's an interesting article on the sulfuric acid market:, and another one from last year . Evidentially, there's been some recent volatility in the market.  It does seem surprising that it costs $100 bucks for a couple kilos, though to be fair, the 10 cent/L value was from 2001, and it appears that $400/tonne is more in line with what producers want (though it was depressed in 2008, and I'm not sure how it's doing now).  I agree, $35 a Liter, or whatever, does seem like a pretty steep markup.  I suppose that the stuff used to make fertilizer probably isn't pure enough to use in a lab, so I'm not sure what type of markup you'd expect there to get lab grade stuff over industrial "good enough" grade. Buddy431 (talk) 03:41, 7 October 2010 (UTC)
 * Chemical economics! The supply of sulfuric acid is inelastic? wow. John Riemann Soong (talk) 03:57, 7 October 2010 (UTC)
 * Isn't that roughly what one would expect, since demand will be almost constant, at least for the scientific grade.   D b f i r s   07:33, 7 October 2010 (UTC)
 * Did you read my articles? The demand for Sulfuric acid is not constant; it rises and falls with the demand for phosphate based fertilizer, its main use.  The amount of acid used in a lab is tiny compared to that used in industrial processes, especially the making of fertilizer.  Additionally, the price of Sulfuric acid is influenced by the price of Sulfur, which does have a more variable supply as old mines are used up and new ones built. Buddy431 (talk) 13:27, 7 October 2010 (UTC)
 * Yes, I was assuming a separate market for scientific grade, as purchased by the OP.   D b f i r s   06:36, 11 October 2010 (UTC)
 * The supply of bulk chemicals is very inelastic, because the factories cost so much to build and, once they're built, cost so much to keep idle. Physchim62 (talk) 08:28, 7 October 2010 (UTC)
 * err, if demand is constant, then elasticity of demand is inelastic. I mean for normal bulk chemicals, I assume if costs plunge or drastically rise factories can allocate good as necessary. They might decide to make perchloric acid instead for example. John Riemann Soong (talk) 09:33, 7 October 2010 (UTC)
 * Also consider quality. I very much assume that the 165 million tonnes is not lab-quality sulfuric acid. Compare water. You can get it for free from every major ocean, but if you want the refined version in your super market, Evian charges several reasonable currency units per bottle. --Stephan Schulz (talk) 07:57, 7 October 2010 (UTC)


 * Most sulphuric acid is very cheap for the reason that most it is produced as a waist product . If you buy non-analytical (which is made by another process in order to maintain purity) industrial acid then is is a lot less.. See Drain cleaner A reasonable mark up for a hazardous product. It is about the same price as this per litre, here  in the UK.--Aspro (talk) 08:20, 7 October 2010 (UTC)
 * As a VERY rough approximation, the price of a laboratory chemical goes up by an order of magnitude for each extra "nine" you want on the purity! Also, if you compare catalogues, you'll see that Sigma-Aldrich are quite expensive as a supplier: they can charge more because of their reputation, and because of the convenience of being able to get just about everything from one place. Physchim62 (talk) 08:32, 7 October 2010 (UTC)
 * This is 95% sulfuric acid though. Not 99.99% sulfuric acid. John Riemann Soong (talk) 19:04, 8 October 2010 (UTC)
 * JRS, you're talking concentration--Physchim is talking purity. You can have a 95% solution that has all sorts of heavy-metal, other-anion, and other-sulfur-oxide contaminants in there too, or you can have certified-analysis ppm-or-lower levels of them. Aldirch lists six half-liters 95-95* concentration at 99.999% purity for US$1250, vs the same 6x0.5L 95-98% concentration of ACS reagent grade (95.0-98.0% purity) for US$213.70. DMacks (talk) 19:38, 8 October 2010 (UTC)

Slit diffraction
When light passes through a slit via Huygens–Fresnel principle, there are waves that encounter the walls of the slit, yes? Does it make a difference whether the walls of the slit absorb or reflect the waves? John Riemann Soong (talk) 04:32, 7 October 2010 (UTC)

I'm also trying to understand the diffraction limit in microscopy -- it's purely due to what happens at the lens, right? That is, if I'm trying to image a 70 nm nanoparticle, we don't have to worry about the interference pattern from the light hitting a rough surface or the reflection pattern of the light hitting a bunch of closely-spaced nanoparticles and we aren't treating the imaged objects as apertures? John Riemann Soong (talk) 05:18, 7 October 2010 (UTC)


 * I think the you should treat the imaged objects as apertures. I do not think the composition of walls of the slit have any impotrance. A ideal slit is of zero length so the walls i am talking about are tha walls facing the source. If the slit has non zero length the reflections from the internal walls will make a difference but then it is not a single slit experiment. --Gr8xoz (talk) 07:59, 7 October 2010 (UTC)


 * If it's not the reflection or absorption of the neighbouring wavelets by the walls I don't know what ultimately generates the diffraction pattern. I mean, you can apply Huygen's principle to light passing through a vacuum (or air). John Riemann Soong (talk) 08:25, 7 October 2010 (UTC)


 * If the wavelength of the light is equal to or less than the thickness of the wall, then the walls of the slit will cause some scattering. If the wavelength is long compared to the thickness of the wall, you can ignore the thickness. Looie496 (talk) 17:36, 7 October 2010 (UTC)

Einstein's view
After read his religious view i still don't get whether he believes in god or not. Second question, did Albert Einstein do not believe in the existence of black hole?174.20.65.111 (talk) 05:58, 7 October 2010 (UTC)
 * Regarding religion: he didn't believe in any god that takes a special interest in the affairs of humans. He did express a reverence for the workings of nature that could be called religious. I don't know what to say beyond that. You might find Albert Einstein helpful. Regarding black holes: I know he didn't believe in them at first, but I don't know whether he ever changed his mind. The understanding of general relativity was still very primitive by modern standards in 1955 when Einstein died—the event horizon, for example, wasn't really identified until 1958 (see Black hole). So probably he never changed his mind, but he might have changed it if he'd lived a couple of decades longer. -- BenRG (talk) 07:03, 7 October 2010 (UTC)
 * Yes. Like many (but not all) scientists and other highly intelligent people that still choose to believe in a god, Einstein's belief system was probably far more complex and nuanced than that of your regular believer. It can thus be very hard to determine exactly what their actual beliefs are, because they are not easy to define in the usual simple yes/no categorisations, and additionally they often avoid sharing the full depth of their personal beliefs in public fora. --jjron (talk) 07:23, 7 October 2010 (UTC)


 * My understanding after I have read the article is that he mostly used god as a metaphor for the overall order in nature and the sum of all natural laws. He did clearly not believe in a god you can interact with. I do not think he believed in an afterlife. He believed in the historical existence of Jesus but not in him being god. He made some ambiguous statements.--Gr8xoz (talk) 07:42, 7 October 2010 (UTC)


 * I presume you've read Albert Einstein's religious views?
 * The answer to your first question depends on how you define the word "god". There is no universal agreement as to what "god" means; there are lots of different conceptions of god.  But I'm guessing that you're thinking of the word "god" in such a way that the answer to your question is "no".  Einstein didn't believe in any kind of a personal god, which eliminates the conceptions of god held by most Christians.  Saying that Einstein believed in god would only be true if you define "god" as just meaning something like "the lawful harmony of the world," or "the sublimity and marvelous order which reveal themselves in nature".  That's not really "god" like I presume you’re thinking of that word. He basically just had a great admiration of nature. Red Act (talk) 07:45, 7 October 2010 (UTC)
 * It's not just a "great admiration of nature," it's more like, "a supreme faith in the notion that nature must be orderly, perfect, and knowable." Which is a bit different. This is one of the reasons he hated quantum mechanics — it seemed un-orderly to him, it seemed necessarily "incomplete" because it claimed that nature wasn't knowable. (Cf. the famous "God doesn't play dice" quip — which really means, "nature doesn't operate in an un-orderly fashion.) It's a form of faith to be sure, but not one that lines up very well with standard conceptions of organized religion. There are echoes of Spinoza through it. --Mr.98 (talk) 11:22, 7 October 2010 (UTC)
 * More than just echoes -- Einstein is frequently (and, for once when it comes to frequently attributed quotes, reliably) quoted as having said "I believe in Spinoza's God who reveals himself in the orderly harmony of what exists, not in a God who concerns himself with fates and actions of human beings." --81.153.109.200 (talk) 18:43, 8 October 2010 (UTC)


 * There are a lot of fairly respectable sites on the internet which say that Einstein didn't believe in black holes. Note that Einstein's belief or non-belief in a scientific theory later in his life is hardly a sign of anything. Oppenheimer quipped at one point that Einstein was a signpost along the way to modern physics, not the path of physics itself (or something along those lines — a signpost of where physics had been, not a lighthouse pointing the way forward, or something). Anyway, in Einstein's day, black holes were nothing more than a few clever mathematical manipulations of the field equations, pushing them to their limits. He didn't think there was a reality to them. Most physicists did not take the idea of black holes very seriously at the time. In the early days of such theory-derived ideas, they are usually treated as mathematical curiosities, but not necessarily as something that exists in nature. (See, e.g., tachyons for a good analog. Do they exist? The theory says that might be able to exist, under current knowledge. But does that mean they must or do exist?) --Mr.98 (talk) 11:31, 7 October 2010 (UTC)


 * I'm not familiar with the history, but that doesn't seem right to me. The existence of black holes is an obvious consequence of the basic principles of general relativity -- if you have enough mass in a region, then light can't escape from it.  There is however a question about whether a black hole contains a singularity at its center -- a point at which the curvature of space becomes undefined.  Straightforward application of the equations of GR do produce a singularity, but many physicists have doubted whether the equations are completely accurate in that regime. Looie496 (talk) 17:33, 7 October 2010 (UTC)


 * What you just said about the singularity is more or less how people felt about (what's now called) the event horizon in 1955. They thought it was a bug in the theory that would go away. It might have been an artifact of the Schwarzschild vacuum's unrealistic amount of symmetry. They didn't have the rotating or charged black hole solutions yet, or the theorems saying that the formation of a black hole is inevitable in certain conditions, or the principles of black hole thermodynamics that make black holes seem like physically reasonable objects. -- BenRG (talk) 19:29, 7 October 2010 (UTC)


 * It's worth noting as well that GR itself is basically unstudied and unhip until the 1950s. The hip things in the 1920s-1940s are particle physics and nuclear physics. It is only in the 1950s that gravity and GR become even standard parts of grad student physics curriculum in anything other than a cursory fashion. --Mr.98 (talk) 20:18, 7 October 2010 (UTC)


 * See Fuzzball (string theory). The mere fact that fuzzballs might be replacements for black holes is sufficient to argue that the existence of black holes has not been proven, except in the vaguest sense of "very dense objects close to the Schwarzschild radius in size". Wnt (talk) 19:57, 8 October 2010 (UTC)


 * As far as I know, fuzzballs are meant to be quantitatively the same as black holes except near the singularity, even inside the event horizon, so they deserve to be called quantum-gravitational black holes. The "fuzzball" description makes them sound different, but there's supposed to be a nontrivial duality à la AdS/CFT between that description and an infalling description. (Even in plain quantum field theory a similar thing happens: you don't encounter any Hawking radiation when falling into a black hole, even though it's certainly there if you don't fall in.) -- BenRG (talk) 23:09, 8 October 2010 (UTC)


 * Which god? Certainly not the god of any religion. 67.243.7.240 (talk) 23:51, 9 October 2010 (UTC)

Why do Some people have heavier sleep than others?
I have noticed that in my family my mother has extremely light sleep (she wakes up to the slightest noises) while me and my father have very heavy sleep and do not wake up very easily. I was wondering why this difference exists. Is it genetic reasons? and if so why? is it based on a particular region of your brain and how it functions? why do some people need deeper sleeps? or could it be an environmental reason depending on whether you grew up in a noisy environment and had to adjust to sleeping through it?Morvarid rohani (talk) 06:48, 7 October 2010 (UTC)
 * In my opinion it's environmental. You get used to sleeping through noise, or you don't. But only up to a limit, I know some people who are hard to wake up even if you shake them, that's probably genetic. So like most questions of this type the answer is: Both! :) Ariel. (talk) 08:30, 7 October 2010 (UTC)
 * There'd obviously be components of both in there, possibly more genetic. For example as a kid I was a pretty heavy sleeper while one of my sisters was a light sleeper. Same environment, but then again also similar genetics. I spose you could proffer the argument that the elder child could be conditioned to quieter surroundings and thus be more prone to be a light sleeper, whilst a younger sibling would more likely be growing up in a far noisier environment and thus tend to be a heavier sleeper. --jjron (talk) 12:03, 7 October 2010 (UTC)
 * Complete speculation and original research, but I tend to notice mothers as lighter sleepers (but not all the time). Could this be down to the urge to protect offspring? Regards, --— Cyclonenim | Chat 17:35, 7 October 2010 (UTC)
 * This is OR, too, but my doctor told me that recent mothers, in particular, awaken easily, for this reason. Comet Tuttle (talk) 20:45, 7 October 2010 (UTC)
 * ... (and more OR) ... I think depth of sleep is probably predominantly a learned behaviour (though there might also be a genetic component).  I find that if I am anticipating a disturbance, or I need to wake at a fixed time, then I sleep much more lightly.  There is also the factor of sleep cycle where depth of sleep will vary during the sleep period.    D b f i r s   02:51, 8 October 2010 (UTC)

Where to focus to photograph a mirror reflection
So say I want to take a photograph of a reflection of myself in a plane mirror. For argument's sake lets assume I'm using manual focus on my camera. Should I set the focus to the surface of the mirror (i.e., the distance from me to the mirror) or to the apparent location of the virtual image (i.e., twice the distance from me to the mirror) in order to get myself in perfect focus? (And yeah, I know I can do a practical test on this, and will sometime, but I want to hear what people have to say first. :) ) --jjron (talk) 07:12, 7 October 2010 (UTC)


 * To take photograph of reflection you must focus on the reflection i.e twice the distance between you and mirror. Focus on mirror if you want to take photograph of mirror surface (scratches, dust etc on surface) - manya (talk) 07:20, 7 October 2010 (UTC)
 * You may find this experiment interesting. - manya (talk) 07:25, 7 October 2010 (UTC)
 * Cheers. That's the sort of thing I tried to find in a quick search myself, but had no luck. Will give this experiment a go myself sometime to try to verify this. --jjron (talk) 12:10, 7 October 2010 (UTC)

Chicken genome nuggets
I heard that the chicken genome on UCSC is going to get updated some time soon-ish. How can I find out how soon? Why can't they just release the information they have instead piecing it together for four years and releasing it in one go? --129.215.5.255 (talk) 09:54, 7 October 2010 (UTC)


 * The UCSC genome browser is a fantastic tool, but I'm not sure if they are directly involved in the chicken genome assembly... Usually the UCSC incorporates genome information after the genome assemblies have been completed by other groups. You could try the NCBI chicken genome page for more info on the chicken genome in particular.  However, as a general rule, each assembly of a genome takes into account a significant amount of new genome data that sometimes results in re-mapping certain parts of the genome that were incorrectly assembled in the previous version.  One consequence is that the numbering of the nucleotides can be dramatically different from one genome assembly to the next, which requires complete re-annotation (or at least conversion of the existing annotations to a new coordinate system).  As you can imagine, this can be a huge computational task.  In order to achieve some degree of stability, those involved in assembly and annotation of the genomes try to batch the new data into relatively comprehensive updates (which can sometimes take months or years).  Plus, the end users of the data would go nuts if the gene coordinates were changing on a monthly, weekly, or daily basis every time a new fragment of the genome were decoded.    --- Medical geneticist (talk) 12:38, 7 October 2010 (UTC)

diffraction of white light versus monochromatic light
Is there a difference in the Fraunhofer diffraction pattern through a slit made if the average wavelengths of the light are the same? What if I have a bimodal distribution of red and violet light, say? John Riemann Soong (talk) 09:59, 7 October 2010 (UTC)

Yes, each wavelength is diffracted individualy, the average wavelengths has no significance. --Gr8xoz (talk) 13:50, 7 October 2010 (UTC)

So why then does white light result in such an orderly pattern, and why do people generally quote the average wavelength of light for microscopy? John Riemann Soong (talk) 15:53, 7 October 2010 (UTC)
 * Because white light, by definition, contains all the wavelengths. Also, white light is something of an ideal.  Just about any real light source is non-uniform light, so not truly "white".  Take sunlight for example, it is actually quite "green", in that there is a greater intensity of light in the green frequencies than other colors.  Incandescent or fluorescent light bulbs will have their own frequency profiles, so in microscopy, the average wavelength is actually a weighted average.  The light source is usually roughly white, in the sense that it isn't missing any frequencies, but the spectrum intensity profile is not going to be a horizontal line, meaning that some wavelengths are more intense than others.  Different light sources will have different profiles.  -- Jayron  32  01:04, 8 October 2010 (UTC)


 * With a single slit of width d you have (in the far field, i.e. Fraunhofer diffraction) maxima at $$sin(\phi) = \frac{\lambda}{d} \cdot 2 n$$ and minima at $$sin(\phi) = \frac{\lambda}{d} \cdot (2 n + 1)$$. If you have "white" light with wavelengths between $$\lambda$$ and $$k \cdot \lambda$$, then the n-th maximum of the longest wavelength will be at a smaller angle $$\phi$$ than the (n+1)-th maximum of the shortest wavelength for $$n < \frac{1}{k-1}$$. For a range from 400 to 760 nm you have k = 1.9, so the first maximum of the red end is still at a smaller angle than the second maximum of the violet light. And the intensity of the maxima declines, the intensity as a function of the angle $$\phi$$ is proportional to $$\frac{1}{sin(\phi)^2} \cdot (1 - cos(\frac{2 \pi d sin(\phi)}{\lambda}))$$
 * Icek (talk) 11:00, 8 October 2010 (UTC)

Pressure cooker - rubber ring
What is the function of ring made up of rubber in pressure cooker apart from sealing the cooker. ...thanx--Myownid420 (talk) 10:30, 7 October 2010 (UTC)


 * It seals the gap between the bowl and the lid so that pressure can build up in the bowl and the temperature of the liquid contents can rise above the normal boiling temperature of water. Nothing else.  Dolphin  ( t ) 10:57, 7 October 2010 (UTC)

Can expressing GFP interfere with any cellular processes?
I'm starting a project whereby I'll try to knockout a gene by homologous recombination (induced by zinc finger nucleases) of a marker such as GFP into said gene. I would prefer to just disrupt the gene by inducing NHEJ since the efficiency should be high enough that selection using a marker isn't really necessary. I don't like the marker method, because I don't trust that expressing GFP doesn't have some (negligible?) effect on the cell. Has anyone investigated (e.g. by microarray or 2D-PAGE) the effects of GFP expression on cell activity? Does anyone share my preference to simply knock out the gene without adding anything or am I just a bionoob? Seans Potato Business 10:50, 7 October 2010 (UTC)
 * Green fluorescent protein has a pretty long track record of being innocuous when expressed at reasonable levels in cells or organisms. There are numerous transgenic animals that express GFP without any obvious toxicity, and thousands upon thousands of in vitro experiments where GFP alone is used as a control to study the effect of a GFP fusion protein.  It is certainly true that when GFP was first being introduced into cells there was quite a bit of concern about toxicity or disruption of cellular processes.  I think that one of the "red" fluorescent proteins was notorious for causing toxicity, but the weight of evidence seems to indicate that GFP is benign.  Of course, massive overexpression of any protein can disrupt cellular processes, but I'd say that your application is pretty safe if you have the transgene being expressed by the endogenous transcriptional machinery or a simple basal promoter. --- Medical geneticist (talk)  —Preceding undated comment added 13:07, 7 October 2010 (UTC).
 * Hmmm, I came up with — is this useful?  This is one of those cases where I think you actually need to use a MeSH topic rather than a keyword to search PubMed for Green fluorescent protein, to get papers about GFP rather than those merely mentioning it. Wnt (talk) 13:10, 7 October 2010 (UTC)

Coin question
Four coins are thrown from a bridge. Coin a is thrown vertically upward, coin b is thrown horizontally, coin c is thrown up at a certain angle with the horizontal, and coin d is dropped from rest. Assume that the initial speeds of coins a,b,and c are equal. Which among the coins will reach the water first? Which will be the last to hit the water? Which among the four coins will hit the water the same time? —Preceding unsigned comment added by 121.54.32.155 (talk) 11:11, 7 October 2010 (UTC)
 * Added new header. --Chemicalinterest (talk) 11:21, 7 October 2010 (UTC)
 * I can give you hints. Which will obviously be the first to hit the water? --Chemicalinterest (talk) 11:21, 7 October 2010 (UTC)
 * This depends enterily on when the different coins are thrown/droped but if they are droped in the given order with enugh time in between then coin a will hit the water first. This is ofcurce only valid if the bridge is over a free water surface. --Gr8xoz (talk) 13:43, 7 October 2010 (UTC)
 * If it's over a temporarily dry Wadi, it depends on whether you stand on the upstream or downstream side, on the angle with the horizon for coin c, and the initial speed for coins b and c. Whichever coin lands farthest upstream will get wet first. ;-) --Stephan Schulz (talk) 15:19, 7 October 2010 (UTC)
 * I can guess the answer the teacher is looking for here, but I don't believe it. Coins have tricky aerodynamics. APL (talk) 15:28, 7 October 2010 (UTC)
 * well, here's a homework hint: making all the standard physics assumptions (i.e., ignoring aerodynamic effects, assuming a flat featureless plain below - though why one would need a bridge on a flat featureless plain is beyond me), you only need to deal with initial velocity in the direction of the pull of gravity. think about it.  -- Ludwigs 2  16:52, 7 October 2010 (UTC)
 * The teacher is obviously assuming a Spherical cow. --Zerozal (talk) 17:58, 7 October 2010 (UTC)
 * ... but a flat Earth. Gandalf61 (talk) 07:45, 8 October 2010 (UTC)


 * splash! splash! That is coins b and d hitting the water simultaneously but the sound of coin b took longer to reach you. Then splash! That was coin c hitting. But wait, what happened to coin a ? Hmmm, can't hear anything. Wait a bit. OUCH! That was coin a hitting your head. Ejecting coins in four different directions at once is difficult and perilous. Cuddlyable3 (talk) 20:46, 7 October 2010 (UTC)
 * As anyone skilled in the art of passive acoustic data processing techniques will tell you, separating the splashes into discrete events so that you can measure the time-delay for each constitutes a mathematically difficult, underdefined source estimation problem. Techniques exist, but if the splashes overlap in any way, you will have to start making all kinds of spherical-cow assumptions about the waveform of the splash.  Nimur (talk) 15:30, 8 October 2010 (UTC)
 * Autocorrelation. Cuddlyable3 (talk) 17:06, 8 October 2010 (UTC)
 * Autocorrelation only works for trivial source estimation cases. Nimur (talk) 20:48, 8 October 2010 (UTC)
 * Indeed. I recorded splashes of coins dropping into a bucket with a sponge at the bottom. In air they produce tiny bursts of white noise that vary in energy down to virtually nothing if the coin enters edge-on. They could not be detected reliably in typical outdoor weather. A hydrophone would do better. A video camera would be the sensor I'd use, with a pond of still water! Cuddlyable3 (talk) 22:45, 8 October 2010 (UTC)
 * I'll treat your question as wanting the real answer, instead of the answer your teacher wants. In that case, the answers should be rather obvious except for coin b vs. coin d.  For a realistic answer to those two, you need the drag equation, which says that the magnitude of the force due to drag on an object is (approximately) proportional to the square of the object's airspeed.  Given that the drag is in the opposite direction of the object's velocity, the upward component of the drag is then proportional to $$v_y \sqrt{v_x^2 +v_y^2}$$, where $$v_y$$ is the downward component of the coin's velocity, and $$v_x$$ is the horizontal component.  From that expression for the upward component of the drag, it's rather clear that coin d will hit the water before coin b, even without doing a full calculation of the equations of motion.  Of course, the preceding assumes that there's no wind.  If there's a horizontal wind, then coin b might hit the water before coin d, if it has a lower airspeed.  Red Act (talk) 01:41, 8 October 2010 (UTC)

Here is a hint. In a vacuum, all bodies at the Earth's surface accelerate towards the center of the Earth at the same rate &mdash; an acceleration of 9.8 m.s-2 or 32.2 ft.s-2. (Bodies made of dense materials such as metals are not significantly affected by air resistance when they are moving at slow speeds so air resistance can be ignored and their acceleration in air can be assumed to be the same as it is in a vacuum.)

All bodies accelerate towards the center of the Earth at the same rate &mdash; even if they are initially moving horizontally at different speeds. For example, imagine a gun aimed horizontally across water. Also imagine a small metal object being held at the same height above the water as the height of the gun barrel. At the instant the gun fires, the small metal object is released and allowed to fall freely into the water. Surprisingly, the projectile and the small metal object both hit the water at exactly the same time because they both accelerate downwards at the same rate &mdash; 9.8 m.s-2. You might say That can't be true &mdash; projectiles from guns take much longer in flight before they hit the ground. The reason for that is guns are almost never fired with their barrels horizontal. The barrel is usually elevated above the horizontal to increase the time of flight and therefore increase the range. But if the barrel is horizontal the horizontal velocity of the projectile will have no effect on its downwards velocity. Dolphin ( t ) 01:50, 8 October 2010 (UTC)
 * The OP should read The Monkey and the Hunter before proceeding. It is a thought experiment which explains nicely the principle being displayed here, plus there's some external links to some nice videos as well. -- Jayron  32  02:08, 8 October 2010 (UTC)


 * In this myth-buster myth they find that the terminal velocity of a coin is less than 65 mph, in vacuum that is reached in (((65 mph) / 2) * (65 mph)) / (9.81 (m / (s^2))) = 43 meter so the approximation that there are no air-drag is only valid for bridges that is lower than approx. 5 m. As Red Act showed so are the horizontal and vertical movements not independent if there are of air-drag. --Gr8xoz (talk) 10:37, 8 October 2010 (UTC)

Metal detectors outside MRI rooms
On Monday I watched the show House, MD on TV and a lady's leg started frying because of some metal pins in it she didn't tell the doctors about. It seemed like such a thing could easily be prevented by simply going through a metal detector on the way to the MRI room. Do real hospitals do this? 20.137.18.50 (talk) 12:16, 7 October 2010 (UTC)


 * Our article MRI discusses some of the dangers and safety measures taken. These types of things are rare and can often be avoided by simple precautions and questions asked of the patient.  The TV show House (as you are undoubtedly aware) is fiction, and as such the producers take certain liberties with medical reality and quite often stretch the truth to make the show a bit more "interesting" for the TV viewer. --- Medical geneticist (talk) 12:21, 7 October 2010 (UTC)


 * Thanks. I agree on the fiction of House and the rarity of MRI incidents. I read the referenced article, specifically "There are many steps that the MRI patient and referring physician can take to help reduce the remaining risks, including providing a full, accurate and thorough medical history to the MRI provider." But at MRI it does say "Missile-effect accidents, where ferromagnetic objects are attracted to the center of the magnet, have resulted in injury and death." and there are references to the actual cases. Those undoubtedly could have been caught by a metal detector. And not checking something so easily checkable since it can often be avoided by simple precautions and questions asked of the patient just seems strange. For instance, I have a blood donor card that is clearly not counterfeit (throw in the odds of who would really go to the effort of counterfeiting a blood donor card) but they still do the test to check what type my blood is. 20.137.18.50 (talk) 13:12, 7 October 2010 (UTC)


 * It's of note that a security metal detector wand (like used in airports) costs only $100-$200. A walk-through metal detector (again like in airports) costs from $3000. I would think that the former would actually be a good investment — cheap, easy to use, and would help with metal that people might not know about (e.g. an embedded BB from childhood that had long been forgotten, or metal shavings from an accident, or something). The latter probably tips the cost/benefit towards cost in all but very large hospitals or facilities. On the other hand, the possibility of false positives might be too high, or, worse, it might open the doctor/hospital up to liability if they have a false negative. Of course, if the rate of accident and danger of accident are both very low, then it wouldn't warrant it. But it strikes me that there would be some patients who either couldn't be relied on to give oral information about such a thing (e.g. the very elderly, or the mentally ill, or children, or the comatose/injured). I would be surprised if they didn't have some kind of technical screening process for them. --Mr.98 (talk) 13:13, 7 October 2010 (UTC)


 * I have walked through many metal detectors with metal on myself such as a belt buckle, keys, and a watch. Having metal detectors that are unable to detect small items of metal would do nothing more than cost a lot of money and create a false sense of security. --  k a i n a w &trade; 13:17, 7 October 2010 (UTC)


 * But you've walked through those ones because the tolerance was set low. You can adjust the tolerance on such machines. If you go through them on a regular basis (as one would working in Washington, DC, where every government building of any size has one), you get used to what they are set to — some are set to go off with pocket change, some you can wear a belt through. Presumably you'd have to figure out how to set their tolerance level to the tolerance level required for the MRI purpose. --Mr.98 (talk) 13:18, 7 October 2010 (UTC)


 * (edit conflich with Kainaw, Mr. 98) How accurate are metal detectors? They're generally made for detecting weapon-size metal objects, rather than metal-shaving size objects.  Weapon-size objects are the types of things that patients and doctors are more likely to know about anyway (medical implants mostly, I suppose), whereas it's metal shavings in the eye, or something like that, that's the real danger in most cases. Buddy431 (talk) 13:20, 7 October 2010 (UTC)


 * Just found out... Metal detectors are very sensitive to MRI machines. So, they have to be kept a good distance from them.  The metal detectors that are "MRI safe" are very expensive and still have issues with reliability when the MRI is in use.  There are ones designed for use in MRI areas, like this.  So, if they manufacture them, some people must be using them. --  k a i n a w &trade; 13:22, 7 October 2010 (UTC)
 * Looks like that one is still intended for keys and change, as at the bottom of the page it says "Metal detectors are not intended to detect metal items or implants inside the body. They will not pinpoint the location or even determine the presence of metal inside the body. A bobby pin in your patient's hair, a key ring in someone's pocket or metal on an item being brought in for use can be discovered with a high-sensitivity detector properly used." 20.137.18.50 (talk) 13:31, 7 October 2010 (UTC)


 * (ec) In general, what you will find is the vast majority of MRI-associated 'projectile' accidents aren't due to concealed or implanted objects, but simple carelessness. Nurses or orderlies don't take care with metal wheelchairs, gurneys, IV stands, or gas cylinders which may contain ferromagnetic parts. Technicians or custodial staff bring a toolbox or floor polisher or other ferromagnetic object into the imaging suite, and stray too close to the magnet. In other words, people usually know when they are bringing metal objects into the room, but fail to take appropriate precautions.  As much as possible, patients will be gowned during the exam, and unable to conceal keys or coins in their pockets.
 * In the case of patients with implanted metal objects, this will usually be revealed by a proper medical history. Where a history is unavailable, where the patient is unsure, or where a patient may have been inadvertently exposed to metal fragments or shavings (a history of metalworking or machining work, for instance) it is standard procedure in most hospitals – particularly for studies of the head – to obtain a radiograph (x-ray) of the area.   This is far more sensitive than the use of an external metal detector. TenOfAllTrades(talk) 13:38, 7 October 2010 (UTC)


 * Do amalgam tooth fillings cause problems or dangers with MRI machines? 92.28.245.77 (talk) 13:27, 7 October 2010 (UTC)


 * Fillings (and other orthodontics) don't generally cause safety issues, but they will tend to interfere with imaging in the area immediately around the metal. TenOfAllTrades(talk) 13:47, 7 October 2010 (UTC)


 * It is my privilege to introduce Reference Desk visitors to this article from the amazing site politedissent.com, in which a medical doctor reviews the medical details of each and every episode of House M.D. On this particular point, the author writes:  "Not to beat a dead horse, but a halfway decent physical exam would have revealed the surgical scars on her shin and the likelihood of an orthopedic repair. A quick x-ray would have confirmed metal pins. At our facility, if the radiologists even suspect some metal in the patient’s history at all, x-rays are ordered."  TenOfAllTrades wins.  Comet Tuttle (talk) 20:20, 7 October 2010 (UTC)
 * Some time back, I had to have an MRI at the Cleveland Clinic, where I was told that bringing objects into the room hasn't been their only problem; one time, their machine pulled in a cleaning cart that was sitting in the hallway. Nyttend (talk) 20:44, 9 October 2010 (UTC)

Seeing through frosted glass or net curtains with a telescope or zoom lens
By focusing on the scene or object of interest beyond, rather than on the frosted glass or net curtains, is it possible to see through them? I expect it is easier to do this the greater the distance between the object/scene and the net cutains, and the nearer the net curtains are to the observer. 92.28.245.77 (talk) 13:25, 7 October 2010 (UTC)
 * To an extent, but you'll still be limited by the opacity of the object - i.e., focussing off in the distance doesn't make something you can barely see through suddenly transparent. An example of where you can do this is something like a wire fence - photographers at events like Formula 1 sometimes have to shoot through a fence, but the fence isn't really visible in the photo. A trick they use which helps even more is to colour in the mesh black rather than leaving it silver as that makes it even less visible in the photo. --jjron (talk) 15:07, 7 October 2010 (UTC)
 * Yes to net curtains; no to frosted glass. For the net curtains, the mesh will not be in focus at the plane of the film in the camera.  Light coming from (reflected by) the curtains will be 'spread out' over the film plane; if the curtains are brightly illuminated then this may reduce the contrast of the resulting image.  On the other hand, the light from the subject – at least, the portion which will pass straight through the gaps in the curtain – can be focused sharply to form a proper image.  Note that the apparent brightness of the subject is going to get reduced in proportion to the fractional coverage of the curtains &mdash; that's how much light is blocked by the curtains and therefore unavailable for forming an image.
 * Frosted glass, on the other hand, diffuses and scatters light. If the light no longer follows a straight path from the subject to the camera, then the lens will be unable to focus it into an image. TenOfAllTrades(talk) 15:50, 7 October 2010 (UTC)

Would it be possible to unscramble an image behind frosted glass,using a laser scan to get the exact 3D structure of the glass? [Trevor Loughlin]80.1.80.10 (talk) 14:40, 8 October 2010 (UTC)
 * You might find this page on Light Fields and Computational Photography interesting. This theoretical problem has been well studied; there are many applications, ranging from commercial-cameras to military and surveillance where the benefits of "seeing through walls" and "seeing around corners" are worth investing a lot of effort.  The reality is, these techniques barely work in laboratory settings, and probably don't work at all in the field.  But they make cool pictures!  This fascinating work on dual photography uses the principal of reciprocity to create images using carefully controlled patterns of light from a projector, and numerically inverting for whatever might be "around the corner" and reflecting it.  Probably the most impressive is the very end of the video (63 MB), where the technique is applied to "guess a card" - imaging a card that is facing the other direction.  Nimur (talk) 23:34, 8 October 2010 (UTC)

Mushroom identification
Anyone know what this is? I origanlly thought it to be the infamous Death cap (Amanita phalloides) but on CommonsWiki someone said that it is probably something else, maybe Amanita gemmata or some other Amanita species. Anyone have any ideas? --The High Fin Sperm Whale 16:59, 7 October 2010 (UTC)
 * It's hard to tell from that picture (can't see the stem or gills) and I'm not sure where you're based, but it looks a bit like Amanita citrina to me. Brammers (talk/c) 18:34, 7 October 2010 (UTC)
 * As you can see from the geocodes, it is in Langley, British Columbia. --The High Fin Sperm Whale 18:47, 7 October 2010 (UTC)
 * Ah, sorry about that; I hadn't thought to look there. Maybe it's worth changing the file description while its species is still not certain? Brammers (talk/c) 18:49, 7 October 2010 (UTC)
 * I think I'll wait until I can tell for sure. Feel free to ask any questions about it. --The High Fin Sperm Whale 20:03, 7 October 2010 (UTC)

Boiling milk in a microwave oven
I was making a hot drink today, and as usual I poured the milk into a glass jug and popped it into the microwave. Just "normal" 2% pasteurised milk. When it was bubbling nicely, I took it out and the milk had separated like happens when it goes off. It smelled bad too. The milk in the bottle smelled fine (and tasted fine) and was not in the slightest bit lumpy, but just to be sure I threw it out. I've never seen milk go off instantly like this. Any ideas as to what happened? --TrogWoolley (talk) 18:28, 7 October 2010 (UTC)
 * Milk burns very easily when heated. Part of it probably burned, and the bubbles spread it around. --The High Fin Sperm Whale 18:48, 7 October 2010 (UTC)


 * The pH had probably fallen slightly and the heat simply sparked the unstable casein complex to precipitate. It wasn't detectable to the taste probably.
 * Milk usually does not smell bad or separate when you put it into a microwave. A cup of milk in the microwave for a minute usually results (at worst) in a thin skin at the top that you only notice when you tilt the cup, that you can just throw out. John Riemann Soong (talk) 03:14, 8 October 2010 (UTC)


 * I've actually encountered the problem before of the milk coagulating/curdling when you warm it. From some discussions I've had, it happens because the milk is starting to go off and so has become more acidic. Acidic coagulation does work better at high temperatures, for example when making paneer you do usually heat the milk first. Nil Einne (talk) 15:09, 8 October 2010 (UTC)


 * thanks. --TrogWoolley (talk) 16:25, 8 October 2010 (UTC)

Red mud into iron?
Can Red mud be refined into iron? (I don't mean physically, I mean practically/economically.) Ariel. (talk) 22:05, 7 October 2010 (UTC)
 * No, because if it could, it would be being done. Companies are not usually in the business of throwing free money away, so if the waste could be refined in such a way as to make more money for the company, they would be doing that rather than leaving it in giant open sewers next to the Danube.  -- Jayron  32  22:14, 7 October 2010 (UTC)
 * I've only got old data immediately to hand, but let's say that the production of iron is 20–50 times greater than the production of alumina (that's probably order-of-magntitude correct). At those sorts of scales, there's no economic incentive to create a new process to deal with this strange "artificial" iron ore rather than using the existing well-known processes on standard iron ore. Physchim62 (talk) 22:25, 7 October 2010 (UTC)
 * I had a thought: We should take this mud and dump it in the ocean. It's alkaline, so it will help neutralize a tiny bit of ocean acidity from CO2, and the iron will encourage algae, which will help reduce CO2 as well. "Red mud: the solution to global warming." Ariel. (talk) 23:28, 7 October 2010 (UTC)
 * Ocean acidity? I thought the ocean was slightly basic. --Chemicalinterest (talk) 23:56, 7 October 2010 (UTC)
 * Ocean acidification. --Tagishsimon (talk) 00:01, 8 October 2010 (UTC)
 * I will refrain from adding my opinion to this discussion and possibly creating a heated discussion. I'll say though, that POV is a joke in the article. --Chemicalinterest (talk) 00:12, 8 October 2010 (UTC)


 * Cheminterest -- your blood can called "too acidic" even when the pH is above 7. See acidosis. The reference point for "acidic" here is NOT when [H+] > [OH-], but when [H+] is just simply too high in absolute terms to be good for living systems. John Riemann Soong (talk) 03:26, 8 October 2010 (UTC)
 * CI: If you have problems with the article, take it to the talk page. Be aware though that the article is going to give due weight to the mainstream consensus and not undue weight to fringe claims like those suggesting anthropogenic climate change isn't happening Nil Einne (talk) 15:00, 8 October 2010 (UTC)


 * Again, the problem is economics. If you just dumped it offshore, the sediment would be a problem: you want it in a fine layer, widely dispersed, just like rivers deliver it... and it's difficult to do that with ships (and even harder with pipelines). If people thought that aluminium was valuable enough to, say, top the Washington Monument with a pyramid of aluminium, then maybe we wouldn't have this problem. Or, maybe, seeing the environmental disasters caused by gold mining, we'd have an even bigger problem. All is speculation. Physchim62 (talk) 00:32, 8 October 2010 (UTC)


 * As one of the refs in the red mud article says: "All processes to separate the metallic contents of red mud (iron, titanium) are not yet economical." That was in 2006, anyway. --Mr.98 (talk) 01:08, 8 October 2010 (UTC)
 * The Washington monument thing was done back in the day before we knew how to refine bauxite into aluminum. Pure aluminum is pretty rare and thus was quite valuable until we could refine the much more common bauxite ore.  Googlemeister (talk) 12:59, 8 October 2010 (UTC)

Is "dark energy" really the Universe's brane whipping around?
I just read a Scientific American article which claims that "dark energy" is really the Universe's brane whipping around, and that this will eventually fold the brane in on itself, converting time into a spatial dimension, which would in turn require everything to move faster than light and thus freeze time. Is it true that the supposed "dark energy" is really a signal that the end of time is approaching? --70.245.189.11 (talk) 22:25, 7 October 2010 (UTC)
 * Well, if there is an "end of time", it's approaching at a speed of about 24 hours per day. However, there are no solid theories about the structure and implications of dark energy yet. According to all we know, the current structure of the universe will remain essentially as it is now for billions and billions of years. Don't expect the end (if any) soon in human terms. --Stephan Schulz (talk) 22:33, 7 October 2010 (UTC)
 * The article said that, if our brane started whipping around, galaxies would appear to speed up in a way that's consistent with observations, and that this would culminate in everything freezing in place because they'd have to move faster than light. --70.245.189.11 (talk) 22:38, 7 October 2010 (UTC)
 * I presume this relates to Membrane (M-Theory) rather than a misspelling of brain. If so, I'm not clear what distinction the OP is bringing when using phrases such as "our brane". Does the article you read have a URL, or was it of the dead tree variety? If the former, do the honours and share it with us, please. --Tagishsimon (talk) 22:46, 7 October 2010 (UTC)
 * By "our brane", I was referring to the 4-dimensional brane that contains the observable Universe. --70.245.189.11 (talk) 22:51, 7 October 2010 (UTC)


 * Current changes in the universe due to dark energy are relatively subtle even when viewed across the whole length and duration of the universe. Regardless of its cause, it is likely that dark energy's effects will remain relatively small for many billions of more years.  Ultimately though it will probably play the key role in determining the fate of the universe, though we can't be sure what that will be until we have a better understanding of dark energy.  Dragons flight (talk) 23:24, 7 October 2010 (UTC)
 * On the other hand, we can be sure that you will pay taxes, and that you will die: we hope that the latter event will be far into the future. Physchim62 (talk) 00:37, 8 October 2010 (UTC)


 * I'm not familiar with the article in question, but what has happened is that some theoretical physicist has written a popularization of his/her latest bleeding-edge research paper and gotten it published in Scientific American. It's no more likely to be correct than the research itself, which is pretty unlikely. Most ideas in theoretical high-energy physics end up being wrong, even the published ones. -- BenRG (talk) 07:17, 8 October 2010 (UTC)
 * Are you saying it's insane in the brane? --Trovatore (talk) 07:26, 8 October 2010 (UTC)
 * Sounds like Eddie's in the space-time continuum again. Gandalf61 (talk) 07:42, 8 October 2010 (UTC)