Wikipedia:Reference desk/Archives/Science/2015 April 3

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April 3

Hentriacontane molecular conformation

Does hentriacontane have a bend in it as shown in the image on the article page? 78.148.106.5 (talk) 00:18, 3 April 2015 (UTC)

No, but neither does it likely have a perfectly straight conformation either. Alkanes have very low energy barriers to rotation, there is basically free rotation around the carbon single bonds; the hydrogen atoms only provide nominal steric hindrance. What this means is that, while the straight chain form is the lowest energy conformation, in reality any bulk sample of such long-chain alkane molecules will assume a bewildering array of conformations at any one moment in time. The bend in that picture is only there to fit the entire molecule in the space provided; lewis diagrams do not actually represent proper molecular geometry anyways. They're a heuristic tool for showing bonding relationships, and do a terrible job of representing real geometry in three dimensions: even more terrible considering the entire molecule is flopping around like a spaghetti noodle, along with billions and billions of its friends. --Jayron32 00:44, 3 April 2015 (UTC)

Thanks, Jayron! :) 78.148.106.5 (talk) 02:04, 3 April 2015 (UTC)

To expand a bit on what Jayron has said, the actual conformation that is lowest energy can depend on environment and is not always the straight chain. For some long chain alkanes (perhaps including hentriacontane, but I'm not sure) the lowest energy conformation is actually bent like in the image in some environments (gas phase and/or aqueous). This is because there can be van der Waals interactions gained by bending or a minimization of the surface exposed to aqueous surroundings. -- Ed (Edgar181) 11:47, 3 April 2015 (UTC)

I was curious and a few seconds on Google turned up the J. Phys. Chem. paper At What Chain Length Do Unbranched Alkanes Prefer Folded Conformations? which states, "Short unbranched alkanes are known to prefer linear conformations, whereas long unbranched alkanes are folded. It is not known with certainty at what chain length the linear conformation is no longer the global minimum". -- Ed (Edgar181) 12:15, 3 April 2015 (UTC)

To expand on the expansion by Edgar, I seem to remember from a 20-year old Organic class that chain length has a lot to do with the equilibrium between annulation and polymerization reactions. IIRC, the standard is that 5-, 6-, and 7- carbon chains are most likely to form rings during annulation reactions; that's because smaller chains have too much ring strain, while longer chains are too "floppy". "Entropically disfavored" was the term used: the chain has too many conformations which don't allow the ends to meet up. I think the same sort of thing is going on here: In any chain of any length, in pure condensed form, the chains "lowest" energy conformation would always be straight-chain staggered conformation, but in reality, given the sheer number of possible conformations for which there is little energy barrier to achieve, the "lowest" energy conformation only represents a miniscule proportion of the total molecules (even if it is the single most common conformation, there's so many others, any one conformation doesn't dominate). It's a statistical thing. --Jayron32 02:03, 4 April 2015 (UTC)

Intermediate taxa

In zoology, what's an intermediate taxon? Mentioned in the title of a source at Embryological origins of the mouth and anus, and appears in lots of Google results, but only one page appeared to give an explanation, and it's both technical (too technical for me) and botany-focused. Nyttend (talk) 13:20, 3 April 2015 (UTC)

My understanding is that it's an outdated term - a bit like missing link. The problem being that all populations are constantly changing and evolving so that describing a particular species as being "intermediate" is a trifle meaningless. Transitional fossil may be useful. Matt Deres (talk) 13:37, 3 April 2015 (UTC)

I'm pretty sure that's not what is meant in the title of the paper Nyttend is talking about here - [1], which describes how their new phylogeny shows "the disappearance of two superphyla". They are basically saying that the new genetic/cladistic/systematics methods show that two previously described unranked taxa (the superphyla) are not supported as meaningful groupings in the new analysis, even though they made sense from a morphological perspective. SemanticMantis (talk) 13:50, 3 April 2015 (UTC)

The paper cited in the first article is just talking about taxa that are not one of the eight major ranks, as well as unranked clades or groupings. Things like superphylum or subspecies or infraorder, fall into the first group of ranks that are not major, and things like Angiosperm or spermatophyta are just not ranked, as described in the infobox. See also Taxonomic_rank and Taxon#Ranks. Part of the confusion is that cladistics and systematics are slowly killing traditional morphological taxonomy, and for the past few decades people have pushed forward better classification schemes that don't fit nicely into the structure of Linnean taxonomy. Note also that botany and zoology use slightly different ranking schemes, so a phylum of animals is equivalent to a division of plants, the the term "intermediate taxon" would mean the same thing in any life science. Does that make sense? BTW that book ref is very confusing; it's not just you. The problem there is that they seem to be addressing both scientific taxonomy and folk taxonomy at the same time. SemanticMantis (talk) 13:46, 3 April 2015 (UTC)

• I can't get behind the paywall, but what they are discussing is not traditional ranks like phylum or intermediate ranks like subphylum, but clades that were found not to fit in the traditional Radiate versus Bilateria dichotomy, and the Protostome versus Deuterostome dichotomy of the eucoelomate bilaterians.

The Radiata include the Cnidaria (jellyfish and relatives) and the Ctenophora (below the Radiata lie the asymmetrical sponges and the placozoa) The Radiata have a mouth, but no anus, and no distinct front and back versus left and right. They have only two body layers, the ectoderm and the endoderm, but no internal body cavities. (Topologically the gut of a jellyfish is open to the outside of the body.

Traditionally, the advanced Bilaterians, including protostomes such as arthropods, annelids, mollusks, and others, and the deuterostomes such echinoderms, vertebrates and others have three body layers, including a mesoderm, which lines a body cavity called the coelom, and a right and left, top and bottom, front and back. The coelem in humans consists of the abdominal cavity in which the intestines and kidneys float, as well as the pericardial cavity.

The deuterstomes and protostomes were assumed to be well defined, and to vary on major themes. The deuterostomes like us formed the anus first, then the mouth during embryology, our nerve cord was dorsal to our gut, and the specifics of the way our early embryonic cells divided, and how our coeloms developed were believed to differ in a distinct way from the protostomes, like the insects, who formed their mouths before their anuses and whose main nerve cord lay below the gut, rather than above it.

But there were "intermediate taxa". Some of the (lesser known) animals with true coeloms shared both deuterstome and protostome traits. The nematodes were considered to lack true coeloms, but also shared the ecdysis form of molting with the arthropods. The flatworms were bilateria, but they lacked coeloms, and also often lacked an anus, so were considered the earliest or a degenerate offshoot, rather than highly evolved.

This image shows the traditional branching of the animal kingdom, with deuterostomes at the top right (yay for us!) protostomes on the top left, and the "lowly" flatworms and roundworms (nematodes) as a primitive sidebranch.

Recently this categorization of coelomate and acoelomate bilateria and the two great branches of protostomes and deuterostomes (which are special because were are deuterostomes) have been reshuffled, with the nematodes closer to the arthropods than the arthropods are to the annelids, with which they were once closely allied because they had segmented bodies.

The flatworms are no longer considered a low coelom-and-anus lacking sidebranch below the protostome-deuterostome split, but are now recognized as closer to the annelids and mollusks.

And the deuterostomes have lost what were once considered intermediate allies like the Brachiopods and other Lophophores to the protostomes, making the deuterostomes a small early branch out of a greater protostome group. Even the validity of the Radiata is now disputed.

It is this reshuffling of once misplaced groups like the flat worms, the lophophorata and the nematodes that is being referred to by the "end of the intermediate taxa":

μηδείς (talk) 01:55, 4 April 2015 (UTC)

Food science question -- evaporation

Resolved

I make chicken soup by adding chicken, vegetables and herbs / spices to about 10 quarts of water and boil it for about 3 hours to make soup. My mother-in-law said that she likes to do a similar thing but boil it for no longer than 2 hours -- otherwise, she says, one needs to add more water (because it boils out). I said that I like the taste of soup boiled for 3 hours or so, and that I counter the problem of water boiling out by adding water. She countered by saying that adding water dilutes the soup. I responded that the only thing evaporating is water (solvent, and not solute) so that by evaporating, the soup becomes more concentrated and all I'm doing is reconstituting it, and so not diluting it at all. And because the pot only holds 10 quarts, there is no way for me to add more water than was originally there, and so there is no danger of actually diluting it. But my mother-in-law remains resolute in maintaining that my soup is watered down and that her method is better. What is the science here -- during evaporation, is anything other than H₂O lost? DRosenbach ^{(Talk | Contribs)} 13:54, 3 April 2015 (UTC)

You will lose some VOC, e.g. some of the aromatic and flavorful compounds in the veggies and herbs. It smells good when you cook it, right? So those molecules came out of the food and into the air. All herbs and spices will change their flavor profile as they cook. If you like the way you make your soup, then you can't be doing it wrong. And you mother isn't exactly right either - she's right that the flavor will be different, but wrong that the difference is because it's "watered down." -On a side note, many recipes call for adding the same spice both early and late, or some early and some late, and this is all to refine how the profiles change as certain compounds are lost or broken down by heat. So you might appease her if you add some more herbs and spices 10 minutes before the end :) SemanticMantis (talk) 13:58, 3 April 2015 (UTC)

Actually it is watered down, for the reason you state: longer boiling removes things other than water. If you add water afterwards, you've got the same volume of water as MIL but less of the other stuff. Nonetheless I agree with SM's advice to appease your MIL... Short Brigade Harvester Boris (talk) 14:51, 3 April 2015 (UTC)

You're right, I was thinking in terms of "VOC depauperate", but for a given fixed volume, that's the same as "watered down" I guess :) SemanticMantis (talk) 15:09, 3 April 2015 (UTC)

Think this is more a case of personal preference than exact science. Two hours of simmering (not boiling) should be enough to tenderize the toughest old bird (the fowl... not the MIL). Science-wise, can I presume that as your brewing up 10 quarts at a time your buying whole chickens? If so then there is a lot of flavor in the skin. Toss all that and other parts you don't want into a pressure cooker:From the Test Kitchen: Perfect Pressure Cooker Chicken Stock Add this about 20 minutes before the soup's done. About the same time that one adds the vegetables (so they retail a little bit of al dente). The herbs could also go in at this time depending on what they are as one doesn't want to loose their aromatic flavor. Cooking With Herbs – When to Add Herbs During Food Preparation. Having said that, it won't prove anything as MIL's will always insist that her soup is better than yours!--Aspro (talk) 16:25, 3 April 2015 (UTC)

Some points:

1) When you add water, assuming it's tap water, you are also adding other things, like chlorine compounds and fluorine. Those could also affect the taste, although the chlorine compounds may boil off, too.

2) Covering the pot to avoid evaporation is one method. However, there are a few caveats with this:

2a) Make sure you have a lid that allows the water that condenses on it to pour completely back into the pot. Many seem to allow some to run down the outside of the pot. Counter-intuitively, a lid that fits snugly is more likely to leak. This is because it allows pressure to build up, then the lid is blown askew by the pressure, letting water drip out then.

2b) Similarly, the sides of the pot can't be so hot that the soup will burn on the inside as it dribbles down. This normally happens if you have a gas stove and the flame is too high, running up the sides of the pot.

2c) A covered pot is more likely to boil over, as it can't dump the excess heat as easily to the air. A much larger pot solves this problem, but it sounds like you don't have one. I have a 42 quart stockpot, for this reason.

3) I agree with adding spices at different times, as some benefit from more cooking than others. However, this also applies to other ingredients. Many veggies might get mushy if overcooked, for example.

4) Bones generally benefit from the longest cooking, as it takes time to break them down. Breaking them up would help a bit, but then you would introduce a choking hazard, unless you grind them all the way down to bone meal. You can reuse the same bones in several batches of soup, to get them the hours of cooking they need without overcooking the rest of the ingredients. StuRat (talk) 19:04, 3 April 2015 (UTC)

To that I would add:

A simmering pot does not boil over.

Yes, vegetables added too early end up mushy -like one finds in tinned food.

Bones, skin and cartilage (all the stuff that one doesn't what to end up in the soup) get quickly broken down in the pressure cooker. Then just strain. [2]. It is a no brainer when the proof of the pudding is in the tasting. This article really goes to town on method How to Make The Best Chicken Stock To that I say... No – just bung it all in! Thinks that Drosenbach should try this, then ask us all over one Friday night to perform a connoisseurs quality test. I will bring my own serviette and a large doggy bag ;-)--Aspro (talk) 20:02, 3 April 2015 (UTC)

A simmering pot can boil over, especially if the pot contains something that foams up, like milk/cream. StuRat (talk) 20:44, 3 Apri

No. temperature is set too high. It is all in the word simmering - below boiling for that particular liquid! Not the boiling point of water, liquid oxygen, liquid iron but milk and cream.--Aspro (talk) 21:28, 3 April 2015 (UTC)l 2015 (UTC)

Thanks -- I learned a lot! DRosenbach ^{(Talk | Contribs)} 19:48, 3 April 2015 (UTC)

You're welcome. I should add to 2a, that some lids have steam ports to prevent pressure from building up. Obviously you lose some water this way, but it's better than the lid sitting askew and water running down the side. As mentioned before, a pressure cooker is even better at stopping evaporation, but I don't like those, as you can't easily add things at different times and stir the pot, and there is some danger of an explosion, although hopefully not if it has a functional pressure release valve. I also like to eat some soup early (say the smaller portions of chicken that are cooked right away), and leave other parts that require more cooking to eat later. StuRat (talk) 20:09, 3 April 2015 (UTC)

Referencing

If you do a physics experiment using film and say when evaluating that the film might have been overexposed and that use of a dark room would prevent this does any of this need to be referenced? It's something a technician told me and I acknowledged the technician in the acknowledgements for his technical advice. 94.3.138.111 (talk) 15:07, 3 April 2015 (UTC)

As usual, it depends on the venue. If it's for a physics journal, it couldn't hurt to cite. Over citing is not usually seen as a problem in modern science as far as I can tell, though many journals do have citation limits. Anyway, something like this [3] is probably almost an appropriate citation for your claim, but a little searching on Google Scholar can probably get you something more appropriate. SemanticMantis (talk) 15:13, 3 April 2015 (UTC)

In general, you should go about it this way. To the readership, any statement you make must either be self-evident, or it must follow from your results, or it must be referenced. If it is self-evident for people who have had a certain education but the readership will also include other people, then a reference to a textbook is usually given. Even specialized physics articles will occasionally give references to quite elementary textbooks when the authors think that may help. Count Iblis (talk) 15:23, 3 April 2015 (UTC)

It follows from the methods which is cited. In the methods I mentioned overexposure. — Preceding unsigned comment added by 94.10.255.6 (talk) 16:32, 3 April 2015 (UTC)

Instruments need to be calibrated and cameras are instruments too. Yes, anything like this, can and should be added to a paper. It is useful because a single experiment is not worth anything until it can be independently reproduced. It helps enormously if these types of practical lab problems are included, as it forewarns other researchers what to guard against when repeating the experiment. OK, you didn't have the resources to redo and get it right – other researchers that follow will be stuck in the same position, in that they have a limited budget and your extra input may lead them to support your theory with what little money they have by not making the same errors – or oversights. Sure, I could have put that more simply but there-you-go.--Aspro (talk) 18:58, 3 April 2015 (UTC)

What is "hydrogenated vegetable oil" ?

Based on my previous Q:

I suppose this is more of a regulatory issue than a science Q, but if they don't say "partially hydrogenated vegetable oil", can it be assumed to be fully hydrogenated vegetable oil ? The lack of the word "fully" makes me nervous. One would think that 0 grams of trans fats would be a way to confirm that, but they can round anything under 0.5 g down to zero in the US, even though 0.5 g of PHVO trans fat in every "serving" would be very unhealthy for you, when they are also allowed to set absurdly small serving sizes. StuRat (talk) 20:22, 3 April 2015 (UTC)

By hydrogenating vegetable oil, manufactures can make it more viscous or by further hydrogenation make it solid like margarine. That is the simple answer. Whether it fully or partial is of no consequence. All hydrogenates are cross bonded and are thus not fit for consumption at any % (percentage). What the US needs is proper regulations where food labels 'state' the actual ingredients rather than what the manufactures would like you to believe are the ingredients.--Aspro (talk) 20:39, 3 April 2015 (UTC)

The cause of the higher melting point of hydrogenated vegetable oil is not associated with crossbonding of the carbon chains. The double bonds make it harder to form crystallin solides because they are not straight anymore. This defects in the structure increase the melting point and this makes olive oil a liquide and tallow a solide.--Stone (talk) 20:49, 3 April 2015 (UTC)

Thinks you have contradicted yourself--Aspro (talk) 21:09, 3 April 2015 (UTC)

That conflicts with my understanding and the earlier answers, that fully hydrogenating vegetable oil eliminates all trans fats. Do you dispute this, or think it would remain unhealthy for some reason other than the presence of artificial trans fat ? StuRat (talk) 20:48, 3 April 2015 (UTC)

Are you thinking that fully saturated fats are fully hydrogenated fats?--Aspro (talk) 21:01, 3 April 2015 (UTC)

For me this reads like:Crossbonding in the oil makes it unhealthy. I doubt that there is a large amount of cross bonding in that fat.--Stone (talk) 20:51, 3 April 2015 (UTC)

Which fat?--Aspro (talk) 21:05, 3 April 2015 (UTC)

Fully hydrogenated means the elimination of all double bonds. In that case, you have produced a saturated fat. Unlike the unnatural form of unsaturated fats that we call trans-fats, most saturated fats can be found in nature, so the resulting saturated fat is probably no more (and no less) unhealthy than eating comparable amounts of naturally occurring saturated fats. Eating large quantities of fat is probably a bad idea in any case, but an additional concern for trans-fats is that the human body doesn't know how to digest it efficiently (because it doesn't occur in nature). Fully hydrogenated products generally won't have that added problem, though you still have typical worries about eating too much fat. Dragons flight (talk) 21:20, 3 April 2015 (UTC)

Are you thinking that fully saturated fats are fully hydrogenated fats or fully hydrogenated fats are the same as fully saturated fats? Your input on this could be important, if your hypothesis overturns everything we know about fatty acids--Aspro (talk) 22:03, 3 April 2015 (UTC)-

As I said, fully hydrogenated fats are a kind of saturated fat. Unlike partially hydrogenated fats (i.e. trans-fats), in most cases fully hydrogenated fats are indistinguishable from naturally occurring saturated fats. You might want to go read some of the articles on the topic because you seem confused about the types of fat and the nomenclature. Dragons flight (talk) 22:20, 3 April 2015 (UTC)

“in most cases fully hydrogenated fats are indistinguishable from naturally occurring saturated fats” Oh, I would love to see your hypothesis. Trans bonds do not become cis bonds due to a bit of food manufacturing magic. Otherwise there would be no issue but there is because their not. I don't know if you have ever hear of the Internet but the explanations are all out there. --Aspro (talk) 22:47, 3 April 2015 (UTC)

Trans/cis bonding is a property of double bonds. Fully converting an unsaturated fat to a saturated fat removes all of the double bonds, both cis and trans. So yes, fully hydrogenating the fat (as opposed to partial hydrogenation) removes the trans bonds. Dragons flight (talk) 23:16, 3 April 2015 (UTC)

• if they don't say "partially hydrogenated vegetable oil", can it be assumed to be fully hydrogenated vegetable oil ? No. According to the Berkeley Welness website, "If the label just says “hydrogenated” oil, you don’t know if it’s fully or partially hydrogenated." Abecedare (talk) 22:54, 3 April 2015 (UTC)

Yes, we need better labeling of ingredients. --Aspro (talk) 23:01, 3 April 2015 (UTC)

That source also confirms Dragon flight's point above, fully hydrogenated oils are not trans fats and don't have the same problems. (It does mention possible concerns over Interesterified fats which are often being used to replace transfats. But of course something with fully hydrogenated fats doesn't have to have interesterified fats. And interesterified fats could be made without hydrogenation even if most probably use some fully hydrogenated fats.) Nil Einne (talk) 23:51, 3 April 2015 (UTC)

As I mentioned in the previous thread (before I saw this one), the Code of Federal Regulations makes it clear that "hydrogenated" means fully hydrogenated and that "partially hydrogenated" must be designated as such. [4] shoy (reactions) 19:20, 7 April 2015 (UTC)