Wikipedia:Reference desk/Archives/Science/2014 August 26

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August 26

Is plasmid supercoiling sequence dependent?

Is plasmid supercoiling sequence dependent?

It will depend on sequence and ionic conditions together. Extreme cases are Z-DNA and triple-stranded DNA formation. Wnt (talk) 17:21, 26 August 2014 (UTC)

Yes, mechanical properties of DNA do indeed depend on sequence, as well as other factors. There is also some relevant info at DNA supercoil and Nucleic acid tertiary structure. Of note "Additionally, certain enzymes such as topoisomerases are able to change DNA topology to facilitate functions" -- e.g. there are enzymes that can add/remove twist, which changes the whole structure. Remember, unless you crystallize it, DNA is a very gangly, floppy thing, and it will take on different structures, depending on what it's doing. Another extreme example is that certain thermophilic archaea have "overtwisted" DNA, compared to "understwisted" supercoils that are prevalent at more normal temperatures. I can't find anything on WP about that, but this paper goes into it a bit [1]. This one describes how positive and negative supercoiling can both be useful, regardless of themophilic/mesophilic status: [2]. SemanticMantis (talk) 18:20, 26 August 2014 (UTC)

Thanks for the interesting article about the thermophilic archaea. So that's how people think the earliest DNA would have evolved and acted, it is quite surprising. Dmcq (talk) 19:30, 26 August 2014 (UTC)

I agree it's interesting, but I'd also be careful with what conclusions we draw. From the article: "Archaea were initially viewed as extremophiles living in harsh environments, such as hot springs and salt lakes, but they have since been found in a broad range of habitats, including soils, oceans, marshlands and the human colon and navel" -- in short, it's not clear to me that the extremophilic archaea are in some sense primitive. E.g. soil archaea may be more primitive, and might have "normal" DNA negative supercoiling. SemanticMantis (talk) 19:57, 26 August 2014 (UTC)

Purpose of naming new chemical elements and small moons

New chemical elements and new moons are named in order to honor scientist/laboratories or gods/deities. However, they aren't very relevant in their respective sciences and people won't use the names very often if at all. Naming makes everything complete although IUPAC and IAU always need much time for it. Are these names ever going to be practical? I think just using numbers would be enough. In Chinese for example, new characters have to be invented for every new chemical element and most Unicode versions don't support characters beyong element 103, so most keyboards can't type them anyway. On the contrary, moons are just numbered in Chinese. --2.246.3.119 (talk) 20:00, 26 August 2014 (UTC)

"Extended periodic table" has an interlanguage link to the Chinese version at zh:扩展元素周期表, which does show names for some elements beyond Z (that is, atomic number) = 103.

—Wavelength (talk) 23:07, 26 August 2014 (UTC)

If you look at that table, the high numbered elements without symbols are "钅" followed by another character, while the more familiar ones have specific characters that combine the two symbols side by side ([3]). But the second characters are symbols that already exist in the language. Wnt (talk) 00:40, 27 August 2014 (UTC)

Exactly. Every metal has the radical 钅 and every element corresponds to only one character. The table you linked above shows two characters for each element from 104 on, which looks very awkward. There may be unicodes for them, but the way the Chinese Wikipedia handled it proves that most computers wouldn't be able to see these new characters, so they decided to break them up into two. Most Chinese dictionaries have the periodic table on the very last page and they always print a new version when a new element has received its name. Of course, the characters won't look odd in dictionaries. --2.246.3.119 (talk) 00:55, 27 August 2014 (UTC)

"A superior man, in regard to what he does not know, shows a cautious reserve. If names be not correct, language is not in accordance with the truth of things. If language be not in accordance with the truth of things, affairs cannot be carried on to success. When affairs cannot be carried on to success, proprieties and music do not flourish. When proprieties and music do not flourish, punishments will not be properly awarded. When punishments are not properly awarded, the people do not know how to move hand or foot. Therefore a superior man considers it necessary that the names he uses may be spoken appropriately, and also that what he speaks may be carried out appropriately. What the superior man requires is just that in his words there may be nothing incorrect."

— Confucius, Analects, Book XIII, Chapter 3, verses 4-7, translated by James Legge loupgarous (talk) 05:53, 27 August 2014 (UTC)

I imagine new elements get named because it's an old tradition and also allows the discoverers to honour whatever or whoever they feel is important to them. Now of course finding new elements gets progressively harder and harder (if you're interested, we simply do not yet have the technology required to make elements with Z > 120), so the naming becomes increasingly important and fraught with significance because you will most likely not get to name all that many elements. And now the work is done in teams, so the team must come to an agreement on this issue which now seems very, very important: it is their one chance to get their desired reference to somewhere or someone onto the periodic table, where it will be remembered forever.

Consider Glenn T. Seaborg's reaction to the naming of seaborgium after him, three years before he died:

"This is the greatest honor ever bestowed upon me--even better, I think, than winning the Nobel Prize," said Seaborg, the co-discoverer of plutonium and nine other transuranium elements. "Future students of chemistry, in learning about the periodic table, may have reason to ask why the element was named for me, and thereby learn more about my work." (ref)

"Element 106" just doesn't feel as significant and important, does it? Yes, it's very short-lived, but it sticks around long enough to do chemistry and form compounds like SgO₃ or [SgO₂F₃]⁻. And what if we reach the island of stability around ³⁰⁶122 and find really long-lived nuclides, perhaps long enough to be practical? It would then get silly to keep calling them by the atomic number – the general public will want a snappier name. (A simple extrapolation of the half-lives of element 113 isotopes would mean that around ³⁰⁵113, the half-lives could get to the ²³²Th or even ²⁰⁹Bi range – this was, I think, first pointed out by Difluoroethene on Talk:Ununtrium. Now, I think the trend will probably turn around sometime in the middle, but I'm not ruling this out.)

Now, I don't know so much about naming new moons. It does create shorter names than the temporary IAU names like S/2007 S 3, but some small Jovian and Saturnian moons have renamed unnamed for years now. Some time ago there was indeed a problem because too many moons were being discovered and there just weren't enough characters from Greek and Roman mythology to be used as names that would fit the rules. So they got widened. I wonder if that might have happened again with the broadened rules? There's also the thing about these new moons being so small (come on, 1 or 2 km?!) that some people feel they shouldn't be called "moons". Double sharp (talk) 08:19, 27 August 2014 (UTC)

Is there any way to disprove the hypothesis that these and other heavy element isotopes with good proton-neutron ratios are already well known, but they're being kept secret because you can make nuclear initiators out of them? Wnt (talk) 18:00, 28 August 2014 (UTC)

Wnt, now you're getting into a seeming conundrum which props up in nuclear weaponeering from time to time - the "well-known secret." Lots of things in Howard Morland's article in the Progressive magazine on how to build a thermonuclear weapon were precisely these "well-known secrets" that the US Department of Energy sued to keep unpublished, at the very same time that they said these "well-known secrets" couldn't be used to make a thermonuclear weapon. But it's indeed well-known (from several authoritative open-source reports) that, say, there's quite a difference from calculated, published critical masses for the "conventional fissiles" (U-233, U-235 and Pu-239) and the lower critical masses attainable if you design and place tampers into the nuclear weapons you make with these fissiles. Just how great a difference in critical mass remains secret knowledge.

Is there any way to disprove the possibility you mention? You've set a two-branched problem:

(a)-Do certain super-heavy isotopes exist whose p-n ratios make them good fission initiators? And if so,

(b)-Is this fact being held secret?

You can't disprove proposition (a) without an improbable amount of research involving cyclotrons and/or other particle accelerators to show that the well-known superheavies in question wouldn't be particularly good fission initiators. Not impossible, but certainly impractical at this time. Later, maybe.

You can't disprove proposition (b) at all. The existence of secrets implies they are, in fact, secret - not known to any but those indoctrinated to the secret knowledge. So disproving the existence of particular secrets... see the issue? Right how, there could be a whole list of superheavy isotopes with the properties you posit in a laboratory file cabinet in Dubna and proving its existence or nonexistence would be a job for Western intelligence.

Finally, there are logical problems with proving something doesn't exist. Check our article Evidence of absence, particularly Evidence_of_absence#.22You_can.27t_prove_a_negative.22. I was tempted to simply say "you can't prove a negative," but it's not as clean as that. As James Randi said, you can't prove a negative, but you can use inductive logic and evidence to assert either existence or nonexistence of an entity (depending on what you want to prove or disprove).

Eventually, you'd have to settle for establishing standards of certainty on your question, then assembling evidence and reasoning toward either a proof or a disproof. Your credibility would depend on the standards of certainty you use, the quality of your evidence and your reasoning. loupgarous (talk) 12:17, 31 August 2014 (UTC)

These are the ones of which the news has come to Harvard/And there may be many others, but they haven't been discarvard. AndrewWTaylor (talk) 13:33, 31 August 2014 (UTC)

Reliable source for vitamin dose suggestions

My experience at pharmacies is that there is a very wide range of vitamin pills sold over the counter. Several brands, many different vitamins, and a wide range of "strengths" of a particular vitamin even within the same brand.

For example, (looking at three brands of Vitamin B Complex), I see Vitamin B6 (biotin) in amounts of 5 mcg, 60 mcg, and 500 mcg per pill. And Vitamin B12 (cyanocobalamin) in amounts of 10 mcg, 50 mcg, and 1000 mcg per pill.

Is there any more or less reliable source to turn to for answers to questions related to vitamin doses? Eg, looking at these products, I can't help but wonder - Is 10 mcg of Vitamin B12 a reasonable amount, in which case 1000 mcg is an absurd, wasteful, perhaps dangerous overdose? Or is 1000 mcg a reasonable amount, in which case 10 mcg is a trivial amount to bother with at all?

Please note I'm NOT asking the reference desk to tell me how much Vitamin B12 to take. I'm asking if there is a reliable source for answers to questions such as this. Thanks, CBHA (talk) 20:36, 26 August 2014 (UTC)

Our Vitamin article contains several such links - this is the one from Health Canada, although the equivalent US table is giving us a 404 at the moment. Incidentally, is "mcg" milli-centi-gram (0.00001 g)? An odd unit, if so. Tevildo (talk) 22:46, 26 August 2014 (UTC)

Quick follow-up - the USDA doesn't seem to maintain its own RDA chart any more, but this is their reference page. Tevildo (talk) 22:55, 26 August 2014 (UTC)

Tevildo, mcg is frequently used in the U.S. for microgram. Deor (talk) 23:06, 26 August 2014 (UTC)

I think it's worth noting that there was a terrible idea to use a non-English alternative to mcg (or the informal but practical "ug") in the scientific literature, namely µg. The problem with this is that for a long time pre Unicode it was typically a lowercase "m" in a symbol font, and any change in the font of a document meant that it became an m. So even in a professionally published scientific paper with no corrections, whenever you see "mg" or "mmol" or "ml" you always have to be wary it's really µg or µmol or µl. And if you see text that's been folded spindled and mutilated through some kind of automated processing into a database, you know it's random. Now fortunately this has been going away by leaps and bounds recently, but I suspect it has taken a heavy toll. For example, I remember I was really suspicious that the factor-of-1000 error that killed the Venezuelan polo team's horses could have been one of those word processing things. Wnt (talk) 00:28, 27 August 2014 (UTC)

Here is another article with added information about the action of and results of deficits of vitamins and minerals. Richard Avery (talk) 07:06, 27 August 2014 (UTC)

The issue with vitamin B12 is that we absorb vitamin B12 using transport enzyms in the stomach. People who are vitamin B12 deficient and who are not strict veganists, do not produce these transport enzymes and they need vitamin B12 injections, or they need to take extremely high dosage vitamin B12 pills as then a small fraction will be absorbed without the transport enzymes.

If you are not vitamin B12 deficient but still use supplements, you should take into account these transport enzymes. Typically, you'll only have a small amount of these enzymes in your stomach which limits the maximum dose you can aborb to about 2 mcg. It is then pointless to swallow a dose that is significantly larger, say 10 mcg. Also, it is pointless to take a vitamin B12 supplement after eating a meal containing a decent amount of vitamin B12. You should take the supplement several hours from eating a meal containing vitamin B12 so that by the time the next vitamin B12 dose enters your stomach the tranport enzmes are again present to be able to absorb the vitamin B12.

You can also decide to bypass this limitation by taking a very large dose. About 1% of the vitamin B12 is absorbed directly without the transport enzymes. So, if you take 100 mcg, you will get about 2 mcg using your tranport enzymes and about 1 mcg will pass through without the tranport enzymes. A dose of 100 mcg will thus yield 3 mcg and 1000 mcg will yield about 12 mcg. Vitamin B12 has been shown to be safe in much larger dosages, e.g. 10,000 mcg is perfectly safe to take. At extremely large dosages you will get Cobalt poisoning. Count Iblis (talk) 18:43, 31 August 2014 (UTC)