Wikipedia:Reference desk/Archives/Science/2018 May 20

= May 20 =

Organic Mechanism Steps
Is this sequence of reaction mechanism steps correct? In particular, in the first step, the reactants contain a cation and an anion (plus a neutral molecule shown over the reaction arrow), but the products show a neutral molecule and a cation. Charge is not conserved, and there are no omitted spectator ions as far as I can see. Looking at the charge shown on the Iodine in Diacetoxyalkoxy Periodinane, the iodine had a positive charge in the reactant and 6 electrons (4 bonds and a lone pair), but then still has the charge in the product despite now having 7 electrons (5 bonds and a lone pair). It seems to me like that charge is not correct. In the second step, it has the opposite problem. The charge disappears from the reactants to the products despite it having the same number of electrons. Again, charges on the left and right don't balance (net positive charge on the left, no net charge on the right). I know sometimes in electron pushing to metals that are undergoing redox the electrons are omitted (since they're not held as lone pairs), but iodine is a non-metal, and the lone pairs are shown. There's no pushing that is summoning electrons from iodine that were previously omitted, or indicating electrons that disappear into iodine. I would think the steps should appear thus i.e. without the positive charge indicated on iodine in diacetoxyalkoxy periodinane. 103.228.155.51 (talk) 01:59, 20 May 2018 (UTC)
 * The first problem is that the original structure of Dess–Martin periodinane is not correct: all three acetates should be bonded to the I. But either way, the result of the first step indeed should have a neutral iodine atom. See our article about the chemical that I linked, or also Dess–Martin oxidation that appears to be an incomplete/overlapping subarticle about the reaction you are discussing. DMacks (talk) 03:26, 20 May 2018 (UTC)
 * Just to support the structural dispute, 10.3762/bjoc.8.172 is an X-ray crystal structure of DMP. DMacks (talk)
 * Oh, that's interesting. I can't find a single other source that depicts DMP as an ionic species. Thanks for that answer. Very helpful. 103.228.155.51 (talk) 03:49, 20 May 2018 (UTC)
 * are you sure that the first ionic structure is inappropriate here? I'm wondering if there might be a "step 0", not shown for this reaction, where the -OAc is lost more or less spontaneously, leaving an I+ to react with something else in an SN1 type reaction.  I suppose the isopropanol could lose a proton first and replace the -OAc in an SN2 type reaction, but I'm not sure you can use such basic conditions on DMP.  (but yes, the I+ on the right side seems like a simple mistake) Wnt (talk) 12:34, 20 May 2018 (UTC)
 * I haven't seen literature support for a pre-dissociation (SN1-like) mechanism. DMP oxidations are usually done in non-protic fairly non-polar solvents (but I cannot find a ref specifically analyzing solvent/temperature effects). Papers examining mechanism/kinetics seem to treat the acetate/alkoxy exchange as a single step for purposes of reaction rate and especially Keq analysis. And 10.1021/jo901841v provides NMR evidence that DMP itself does not rapidly exchange acetate with added acetate in solution, but instead finds distinct non-equivalent (non-exchanging) acetates on the I. Instead, that ref supports exchanges of the I on the two O of acetate is rapid via an intramolecular shift (tighter not looser attachment of them?). DMacks (talk) 13:46, 20 May 2018 (UTC)

What is sodium nucleotide?
What is Sodium nucleotide? I saw it in a list of choices as a part of MCQs about blood components... but when I googled it I found a little bit information about it (something like 250 results on Google!), so I had a thought that maybe it is known in another name? --93.126.116.89 (talk) 10:32, 20 May 2018 (UTC)
 * We literally have an article on nucleotides. Plasmic Physics (talk) 11:47, 20 May 2018 (UTC)
 * The term seems unfamiliar, but I assume that they mean something like ATP disodium salt . Nucleotides contain phosphate groups, which are related to phosphoric acid; hence they are not usually neutral at physiological conditions but carry a negative charge (which is of relevance to DNA melting, etc.)  Which means that if you try to isolate them from solution, some kind of counterion must be present, and in extracellular environments or saline buffers etc. that would most often be sodium.  That said, there are other counterions present in such situations, which will be mixed together as the nucleotide is isolated to bring things to a net neutral charge, and I wouldn't ordinarily think to say "sodium salt of a nucleotide" about something unless it had been synthesized or purified. Wnt (talk) 12:20, 20 May 2018 (UTC)
 * Well, you know, an incorrect answer on a multiple choice quiz doesn't necessarily have a specific meaning. In the literature "sodium nucleotide" usually refers to a salt formed by combining sodium with a nucleotide. Looie496 (talk) 15:05, 20 May 2018 (UTC)
 * An incorrect answer ("distractor") on a multiple-choice quiz doesn't necessarily have to have any meaning in context, be self-contradictory, or even be actual words at all. After all, they are, by definition, "not correct" for the context. Just off the top of my head, goofy choices might be added when a test-writer needs one more option but can't think of anything else plausible, as a "freebie" hint for random-guessers who even have a slight idea, as tension-breakers to make students smile when reading a difficult exam, or just to see if they can catch someone who is truely clueless. DMacks (talk) 16:30, 20 May 2018 (UTC)

Brain wiring
Why is the brain wiring not as optimized as possible? And even 'twisted'? That is, left hemisphere connected to right side of the body and right hemisphere to the left side (more or less)? Why is the visual cortex quite on the back of the brain, wouldn't the neuronal connection be safer closer to the eyes? Wouldn't simplicity be a clear evolutionary advantage? Less stuff means less stuff that can go wrong. --Doroletho (talk) 17:22, 20 May 2018 (UTC)
 * How do you know that it is not optimized? Ruslik_ Zero 18:37, 20 May 2018 (UTC)


 * Our Contralateral brain article discusses some theories about the evolution of this feature. Be careful not to assume that this is something other than the end result of smaller changes. Some of them early on may have had a clearer "reason" with no obvious drawback, and once there became some drawbacks, the cost of getting out of that evolutionary rut was too great at that time. DMacks (talk) 19:01, 20 May 2018 (UTC)


 * The answer to "Why didn't evolution find this better way?" is always: there's no chain of incremental changes, leading from one to the other, such that each step is an improvement. —Tamfang (talk) 19:32, 20 May 2018 (UTC)
 * Well, not quite always. It's also possible that the existing form is too new for the necessary mutations to have happened (and been selected for) yet. --76.69.47.55 (talk) 06:27, 21 May 2018 (UTC)
 * Because evolution works on the basis of "good enough". See argument from poor design; the examples of "suboptimal" design in nature are legion. As long as an organism can survive and reproduce, its traits can make it to the next generation. Traits that are only somewhat suboptimal will only be slowly acted against by selection pressure. It's also difficult for evolution to "go back" and "undo" a bunch of traits to replace them with something "better". If an organism is at a local maximum in the fitness landscape, it's very unlikely for evolutionary pressure to push it "downhill" in order to get to another "peak", even if said peak is higher. The usual outcome instead is gradual tinkering with existing traits, which often leads to exaptation of a trait for something else. --47.146.63.87 (talk) 13:42, 21 May 2018 (UTC)
 * Here is a reference on evolution of the optic chiasm - one surprising detail is that some humans have achiasmatic syndrome aka nondecussating retinal-fugal fiber syndrome; they can see but have congenital nystagmus, involuntary horizontal movements of the eye. From this paper it looks like the tracts don't cross over, at least in one case.  Curiously, that one says there is "mirror reversality" because the nerves from the side of the eye that should cross over end up aligning with others from the opposite side.  But I don't know if that means that the person actually sees the world superimposed with a mirror image or not; I don't think so because the same paper says that gross vision is maintained.
 * In a broader context I should note that the pineal gland is, in some vertebrates, a dorsal eye. The optic tracts enter the thalamus at the dorsal side.  The superior colliculus integrates optic information dorsally in the midbrain just below the thalamus.  And the eyes are originally derived from the brain, a dorsal structure.  It seems, therefore, that there should be a deep dorsal evolutionary origin for eyes, but I haven't seen a good model for how it would once have worked. Wnt (talk) 14:56, 21 May 2018 (UTC)


 * Some book I read decades ago, perhaps by Asimov, speculated that having the right side of the brain connected to the left arm, leg and eye might help you fight an attacker who is to your left and who whacks the left side of your head, rendering the left brain less effective. Seems like that would rarely be an advantage to the wild animal who also have the crossover like it would be to a human fighter. Edison (talk) 17:03, 21 May 2018 (UTC)


 * I don't see how, in the case of a brain damage, it could matter what side was and to what it was connected. Hofhof (talk) 00:51, 22 May 2018 (UTC)


 * If the attacker is to your left and conks the left side of your head, and the left hemisphere of the brain is impaired as a result more than the right side, then per the writer, the less damaged right hemisphere could direct the left arm to punch him back. “Brain damage” is not always necessarily to the same extent throughout the brain. Please email me if you need further explanation of concepts such as localized injury to brain tissue. . Edison (talk) 03:06, 22 May 2018 (UTC)


 * No, I'm afraid Hofhof's objection cannot be that easily dismissed. 1) Only an insanely tiny fraction of TBIs sufficient to create significant brain damage are going to specifically impair just contralateral motor function of the specific extremities needed to defend one's self, while leaving the individual otherwise mostly unharmed (and certainly, able to survive, because the survival part is a precondition of the argument that this is a selected-for pressure). That's just not remotely the way brain injuries work. 2) Weighed against the collective pressures on brain anatomy and neurophysiology, even if there was a selective pressure here, it would not have been sufficient enough to have selective value when balanced against the overall structures/modules which have arisen because of much greater pragmatic benefit.  And 3) hemispheric development began weeeeelllll before humans in vertebrate history and is common to many animals which can expect no great incidence of head trauma, much less the sort which would require the creature to thereafter bob and weave around an opponent attacking from a given side. Nor is there a correlation between creatures with greater susceptibility to head trauma and increased hemispheric isolation of motor function.


 * So yeah, whoever your "expert" was, they were practicing pure folk neurophysiology. It could have been Asimov, frankly.  I adored the man, but he came from an earlier era when popular science gurus were expected to comment on a wide array of topics and sometimes found themselves stranded when going out on a limb.  And boy did Asimov like to speculate; indeed, that ceaseless wonder at every aspect of the human condition that science could inform upon was part of his charm, and something then-contemporary popular science culture was more tolerant of, thirty to fifty years ago.  But today, we know a lot about the selective pressures which are thought likely to have lead to hemispheric physiology, and no serious researcher has ever suggested the theory you discuss above as being anywhere on the map of commonly contemplated selective features for this quite major aspect of brain physiology. Snow let's rap 03:09, 23 May 2018 (UTC)


 * OP, I would advise against ever analyzing adaptive fitness through the lens that it needs to move an organism towards more "optimized" or "perfect" form, especially when it comes to neurophysiology. Organisms are only "optimized" in the sense that they are calibrated towards their particular ecological niche, and therefore are more likely to survive in the environment and contexts they are likely to face. But as a more or less per se matter, all useful adaptions have trade-offs, and this most certainly applies to brain structure.  The brain (with regard to organisms with developed cerebrums in particular, but also other vertebrates) is also highly modular; it has many different structures which developed under separate (if sometimes overlapping) pressures, and generally controlled by different genes, meaning they sometimes work at cross purposes, competing (in a manner of speaking) at fulfilling the function of their design, as each was arrived at because it conferred some evolutionary advantage in some context.  Even if the brain were not modular, it would (in the context of its adaptive value to all vertebrates) still need to find some way to be (to varying extent amongst different species) something of a generalist, because it needs to be able to process unpredictable stimuli and meet a wide variety of practical challenges, and the nature of existence for all organisms (particularly those of great complexity) is that they can't know in advance exactly what problems they will be facing in every instant of their life.


 * So most brains are highly optimized in the sense that they prepare the specific organism they are a part of to face the challenges that it is likely to face--or more precisely, which its forebearers did in fact face. While at the same time, optimization outside of the terms of context/ecological niche is a more or less meaningless concept.  There are some fields of the cognitive sciences which are completely predicated on these principles; for example, with regard to human hebaviour, there is evolutionary psychology which attempts to explain some of our more peculiar and sometimes counter-intuitive-seeming propensities as a product of our genetic heritage (which, unless you are an animist of some sort, you must do if you want to be rational about human nature).  According to the general thrust of EP, these "irrational" behaviours are the result of the operation of modules which developed as part of our genetic heritage, and because very little time has passed in evolutionary terms since we became behaviorally modern humans (meaning that we have not "evolved" much in the "mere" 100,000 years or so since), our hunter-gatherer brains still make many decisions which are not yet perfectly adapted to the advantages of our new developed societies/ecological context.  So, simply because we have come so far so fast in terms of changes to our environment (social and technological) we sometimes behave in a manner that is not 100% conductive to our own well-being as modern humans, but in a fashion that was quite optimized to our original context as the third chimpanzee. To use a (somewhat inaccurate) metaphor, we have software that is just a little too out-of-date to make perfect use of our hardware, without bugs.


 * Lastly, your final proposition there deserves special mention, because you are quite right that sometimes the simplest design is the most optimal for an organism, including with regard to its nervous system. So, many species are highly optimized (and highly successful in terms of longevity of the species in a more or less unaltered state for up to hundreds of millions of years or more) to their environment despite having relatively simple brains.  But some of their offspring or distant cousins found themselves in contexts where random mutations and adaptive pressures caused them to adopt traits which allowed them to discern between a greater number of stimuli or to adapt to a wider variety of challenges.  Then some of the offspring of these organisms (with their brains that were necessarily just slightly more complicated than their forebearers) also went on to even further grow their brain complexity, and so on, and so on.  Some of them also occasionally traded back their complexity for simpler designs again, because their environment demanded it (although this happens less frequently for very complex reasons I won't go into here).  What you are left with at the end of the day (err, epoch) is is a huge array of different species with greatly varying neuro-complexity (and very different specialization of its structures even among the highly complex varieties), each according to its ecological niche.  I hope that helps address some of your questions--feel free to ping if you have follow-ups! Sno<b style="color: #b2dffe;">w</b> <b style="color: #d4143a">let's rap</b> 04:08, 23 May 2018 (UTC)


 * Mostly sensible, but what does animism have to do with Young Earth creationism? I wouldn't even expect animists to hesitate about evolutionary ideas, though I should admit I don't know their religion. Wnt (talk) 14:04, 24 May 2018 (UTC)


 * I meant "animist" in the more traditional and broad sense; i.e. as regards a belief that human nature arises from spiritual forces and entities, rather than purely naturalistic mechanisms. I'm afraid I don't follow the young earth creationist reference, as it relates to my comments. <b style="color: #19a0fd;">S</b><b style="color: #66c0fd">n</b><b style="color: #99d5fe;">o</b><b style="color: #b2dffe;">w</b> <b style="color: #d4143a">let's rap</b> 08:25, 25 May 2018 (UTC)


 * If we have an article about the broader sense you describe, could you add it to animism (disambiguation)? Thanks. Wnt (talk) 13:25, 25 May 2018 (UTC)


 * Well, the closest thing we have is the main animism article; that article approaches the concept from three overlapping usages: 1) animism at its broadest sense (any kind of belief in a supernatural force which infuses the physical world and is said to be the ultimate source of life, or thought, or spiritual vitality; as a tautological matter, some of these beliefs are said to be more dualistic than others, but for purposes of the philosophy of cognition, I personally think they all qualify as at least somewhat dualistic--though you will find that article gives voice to opinions which disagree with me on that point), 2) animism as it is utilized as a clinical term in anthropology and some other social sciences to describe a subset of spiritual beliefs, and 3) specific religious traditions which have called themselves "animism" or described themselves as "animistic" (often, but not exclusively, new wave spiritual movements or modern versions of traditional shamanistic beliefs). Each of the three uses converges on a common center, but the second two are each a little more narrow than the usage that precedes it on that short list.  My usage is a little dated, but still out there; its just a way of saying "a belief or argument which is inconsistent with a strict naturalistic view", or, put otherwise, any belief or argument which diverges from an explanation predicated in a belief that all things are a part of the natural universe and should (in theory) be explainable purely by physical laws, even if we don't as yet understand all of those laws. <b style="color: #19a0fd;">S</b><b style="color: #66c0fd">n</b><b style="color: #99d5fe;">o</b><b style="color: #b2dffe;">w</b> <b style="color: #d4143a">let's rap</b> 23:38, 25 May 2018 (UTC)
 * I may have been misunderstanding you from the beginning. You weren't suggesting doubt of evolution in general, necessarily, but of the role of genes in psychology, which is (among other things) a more debatable topic.  We have the strange phenomenon of "general intelligence" and what, to the non-animist (in your broader sense) must be a very surprising deficit of "criminal genes".  Why aren't there races incapable of working mathematics, or families with a mappable locus for committing violent crimes?  It is conceivable that there is some middle ground between naturalism and animism where people admit that a natural process leaves the human essence somehow in command of its destiny - "emergent phenomena" being the vague yet perhaps insufficient description often used. Wnt (talk) 14:55, 26 May 2018 (UTC)
 * No, neither of those interpretations is quite what I meant with my reference to animism there. What I was saying was that any person who wants to understand human nature as a purely naturalistic phenomena will necessarily have to contend with the massive role which genetics (and thus our collective history of selective pressures) play in that story, and I was emphasizing the importance of that role by saying that only those people who by definition divorce their analysis of the question entirely from naturalism can afford not to contemplate the evolutionary factor prominently; for those undertaking a scientific/empirical analysis of brain function and the phenomena that arise from it, it is a necessity.


 * In any event, to answer your question, I think, as an outright per se matter, naturalism and animism are indeed counter-indicatory philosophies; as a definitional matter, naturalism rejects the existence (or relevance of speculation to) anything beyond the physical universe; that is its foundational concept. And also as a purely definitional matter, animism is the belief in a force (or entities, or what-have-you), which act upon the physical world from beyond it.  Emergent phenomena are completely consistent with a purely naturalistic philosophy. They might also be completely consistent with an animistic belief system, but because the forces are said to be beyond the observable universe and not subject to its physical laws in important ways, you can pretty much say anything about the relationship between an animistic force and something in the physical world, because you can't empirically test it.  That's the entire point of having the distinction between a naturalistic and animistic view.  <b style="color: #19a0fd;">S</b><b style="color: #66c0fd">n</b><b style="color: #99d5fe;">o</b><b style="color: #b2dffe;">w</b> <b style="color: #d4143a">let's rap</b> 05:16, 27 May 2018 (UTC)