Wikipedia:Reference desk/Archives/Science/2009 March 12

= March 12 =

Chemical reaction writing programs
Anyone here know of any good (preferably free) programs for drawing chemical reactions, with lewis bonds, electron pushing, etc? (PS: I use Windows). Thanks. Someguy1221 (talk) 04:51, 12 March 2009 (UTC)
 * I recommend ISIS/Draw and MarvinSketch to my organic students. DMacks (talk) 05:02, 12 March 2009 (UTC)
 * One way or another ISIS/Draw was acquired by Symyx (I think when Symyx bought MDL for their electronic notebook). In any case ISIS/Draw doesn't appear to be freely available anymore.  Molecule editors appears to have a few example of open source programs.--OMCV (talk) 05:52, 12 March 2009 (UTC)
 * There is a Symyx Draw no-fee version. Obviously not free-as-in-speech, but still no-cash-outlay-to-use. DMacks (talk) 06:05, 12 March 2009 (UTC)
 * Thanks, with ChemDraw move to a license model I might end up moving back to ISIS someday soon.--OMCV (talk) 06:08, 12 March 2009 (UTC)

Heat in the human brain
Does the human brain, like a computer's CPU, produce heat at a rate proportional to the rate of processing it performs? Neon Merlin  05:10, 12 March 2009 (UTC)


 * Increased blood flow is very well correlated with increased neural activity (see Functional magnetic resonance imaging) but it's not clear what the purpose is. It'd be awesome if we could say that increased firing rates of neuron's caused an increased use of oxygen (and by extension, an increase in heat, not that that's what neuroscientists care about, to my knowledge). But as the article explains, it's not nearly that simple, and is still being actively researched. Someguy1221 (talk) 05:59, 12 March 2009 (UTC)


 * this may help I don't have a pubmed access card anymore (but if you go to university, it is free to get one. 71.54.173.193 (talk) 10:57, 12 March 2009 (UTC)
 * Furthermore, it doesn't have to do with "processing", it simply has to do with brain metabolism. I asked that question several months ago and is an active area of research.  I am not an expert, just a hunter-gatherer of knowledge.  When the brain oxidizes glucose, heat is released.  When your brain is active in say the PFC, then that area uses more glucose.  If you want to get your brain hot, perform an activity that is in your rote memory (i.e. you can do it without thinking about it), and do that while trying to do 4d maze puzzles online.  The physical activity should be something very light, such as spinning a poker chip in your fingers.  If you try to "light up" all the areas of your brain, you can feel very sleepy afterwards.  however, its not something that can be measured.  If you want a really long post of the subject, its actually one of my favorite interests in neurology, just let me know.  I always liked the idea of brain analogies to computers.  You seem to be coming from the computer side, while I'm coming from the opposite side (biology major).  I'm just a noob, but I know how to use google-scholar, which has tons of technical stuff that is a lot to digest.  Most of the stuff is talking about neuroactive drugs; rarely do you find a purely purposeful article written about a fun, interesting topic.  —Preceding unsigned comment added by 71.54.173.193 (talk) 11:06, 12 March 2009 (UTC)
 * OK - I'll bite! I'd like a really long post on the subject please. It seems relevent to this question - and it's certainly of more general interest. (Besides - I need to point at someone else when people complain that my posts are too long to read!)  There is a rather fundamental relationship between information flow and thermodynamics.  Ties between the dual concepts of "Entropy is about heat" and "Entropy is about order and randomness" seem to be fundamental.  Hence, I would certainly maintain that it's impossible for "thinking" or "computing" to happen without generating heat.  However - computers get hot when their transistors are switching - so if your computer just sits there idly flipping registers and memory between 10101010 and 01010101, it'll get hot without actually doing anything meaningful.  It's interesting that instructing your hand to spin a poker chip over and over does the same thing in humans. SteveBaker (talk) 15:39, 12 March 2009 (UTC)
 * See Landauer's principle for the minimum amount of heat generated from computation. Also, see Reversible computing for getting around that problem by never actually deleting anything. I'm pretty sure it would still generate some heat because something would have to move and leave gravitational waves, though. — DanielLC 17:14, 12 March 2009 (UTC)

Rhesus incompatibility
Why is it that hemolytic disease of the newborn only occurs when a mother is rhesus negative and her baby is rhesus positive? Why does the same thing not occur if the mother is Rh positive and the baby is Rh negative? Many thanks in advance. —Preceding unsigned comment added by 139.222.241.23 (talk) 12:24, 12 March 2009 (UTC)
 * If an Rh -ve mother gives birth to a Rh +ve baby, it is relatively common for a small amount of the fetal blood to enter the mother's circulation at around the time of separation of the placenta. This causes the mother to manufacture antibodies to the Rh factor.  If she gets pregnant again, those antibodies she made last time can cross the placenta and enter the fetal circulation, and if that baby is RH +ve also, the reaction of the mother's antibodies to the baby's Rh factor causes HDN.  So that's why all Rh -ve new mums are given Anti-D - to prevent those antibodies forming.  If the mother is Rh +ve she is essentially already immune to the Rh factor and so no antibody forming process occurs, so no problem for the baby.   Matto  paedia  Have a yarn  12:46, 12 March 2009 (UTC)
 * A Rh -ve baby could come into contact with a Rh +ve mother's blood and develop the antibodies, which I guess would increase the chance of haemolytic disease of the newborn occurring if that baby grows up and have a Rh +ve baby. The original baby wouldn't be at any risk, though. --Tango (talk) 13:49, 12 March 2009 (UTC)


 * Are you sure about that? Wouldn't the baby's immune system be to immature for that to happen? Dauto (talk) 16:00, 12 March 2009 (UTC)
 * No, I'm not sure. If it does happen, the risk is probably very low. I know there are other ways to become sensitised to the Rhesus D antigen than just during childbirth (mistaken transfusions, for example), but I don't know if during your own birth is one of them. Newborn babies certainly have a working immune system - they wouldn't last very long without one - they need help from their mother's immune system (via the placenta and breast milk) because they haven't been exposed to anything yet so don't have their own antibodies, but I think they are capable of making their own when they are exposed to something. --Tango (talk) 16:13, 12 March 2009 (UTC)


 * Looked at another way (very simplistically), the Rh-neg baby lacks the antigen, so there is nothing for the mom's immune system to attack. --Scray (talk) 15:45, 12 March 2009 (UTC)


 * Dauto is correct. Rhesus disease is modulated by the adaptive immune system, notably B cells and T cells. B cell function doesn't mature for at least several months after birth, possibly up to two years. Memory B cells are required to maintain long-term immunity; these are absent in the fetus and new-born. Similarly, T cells develop in the thymus which matures during childhood. Colostrum, a form of breast milk, contains antibodies that assist immunity in the new-born infant. Axl  ¤  [Talk]  16:29, 12 March 2009 (UTC)

Thanks to all who helped! —Preceding unsigned comment added by 139.222.241.23 (talk) 20:55, 12 March 2009 (UTC)
 * There are two "rhesus molecules". The one with the D epitope, which is highly immunogenic, and the one with the c or C and e or E epitopes, which are less immunogenic. Persons who are Rh(D) negative lack the entire Rh(D) molecule. Antibodies against all of these five "rhesus epitopes" may cause HDN, but anti-D immunization is much more frequent than the others, and is a much greater problem (with anti-c as number two in the Rh-system). HDN is caused by maternal immunization against fetal antigens. The hypothetical immunization of an Rh(D) negative baby against Rh(D) positive maternal blood that Tango suggests may cause problems later in the life of the baby, is not something that is seen in clinical practice. If anything, the entry of maternal blood cells into the circulation of the fetus or newborn would lead to tolerization, not immunization. --NorwegianBluetalk 22:29, 12 March 2009 (UTC)


 * "Reese's incompatibility" = not liking peanut butter in your chocolate. StuRat (talk) 05:44, 13 March 2009 (UTC)

What is the usefulness of hESC compared to Adult stem cells
We're soon going to have a speaker at our school speak on ESC research and related topics. He is a theology professor and I have a nagging feeling that the information he gives at the talk won't be the full, or the accurate, picture. This is one issue which frequently comes up in the discussion and I'm wondering how stem cell research rates these two types of stem cells (feel free to include information on umbilical cord stem cells as well) in reference to their potential usefulness. I do understand that adult stem cells have already been used for some purposes, but my question is on the expected utility of these two types of cells. I have no interest in any analysis of what "should" be done, just what those who are in the field realistically believe "could" be done by each of these two sources.

If I didn't have such a large amount of work on my plate I would do a thorough look into this myself, but I imagine someone here already can cite numerous journals and studies without too much effort.

Thank you :)

Chris M. (talk) 17:43, 12 March 2009 (UTC)
 * Try HESC and Induced pluripotent stem cell. Kittybrewster  &#9742;  20:49, 12 March 2009 (UTC)

Tomentella Fungus and Dicrocoelium dendriticum
Dicrocoelium dendriticum causes the ant (forgot which species) to climb a grass blade every night and climb down at day. And the Tomentella Fungus causes the ant to perch high on a blade of grass and the fungus grows out of its head into a spike which then spits out spores to infect other ants (ew!). Could this ever happen to humans? or has it?--Emyn ned (talk) 18:21, 12 March 2009 (UTC)

I meant more of the mind-controlling like. Or whatever else... --Emyn ned (talk) 18:25, 12 March 2009 (UTC)


 * I think there's a parasite that makes you want to touch your mouth after going to the toilet. —Preceding unsigned comment added by 124.176.181.108 (talk) 19:00, 12 March 2009 (UTC)


 * See Toxoplasmosis for one example. -- Coneslayer (talk) 19:05, 12 March 2009 (UTC)

Oh, that's a good example! --Emyn ned (talk) 19:34, 12 March 2009 (UTC)


 * I think rabies has some neurological symptoms in humans that might fit your mind-controll description, depending on how broadlly you define mind-controll. Dauto (talk) 19:27, 12 March 2009 (UTC)

So, do you think that anytime soon, we will witness someone climbling a tree, have a cone grow out of his head and ooze out spores to other people below? --Emyn ned (talk) 19:35, 12 March 2009 (UTC)


 * Probably - EronTalk 19:49, 12 March 2009 (UTC)


 * I would say no, because those microbes are likely only able to activate existing programming in the brain. I suspect that those ants already had a "program" to climb a blade of grass, perhaps to view the surrounding area or communicate with distant ants.  Similarly, animals with rabies already had a program to bite other animals.  People do have such basic "instinctive" functions, but they tend to be for very simple things, like coughing, vomiting, hiccups, etc.  Therefore, things like this could indeed result from a brain parasite.  However, climbing a tree isn't instinctive for us, it's a learned behavior.  This means it's learned differently, if at all, for different people, as opposed to a simple program that can be easily activated by a brain parasite. StuRat (talk) 05:40, 13 March 2009 (UTC)

So, it is possible that someone with "chronic hiccups" could actually have a brain parasite? Is it possible that it could have gone undetected by doctors looking for a diagnosis? Maybe everyone's brain is infected by millions of different types of parasites responsible for altering specifc behaviors?! --Emyn ned (talk) 13:23, 13 March 2009 (UTC)


 * I don't know of any cases where a parasite causes hiccups, but star fruit can do this in people with kidney failure: Star_fruit. StuRat (talk) 14:57, 13 March 2009 (UTC)

Thanks everyone. Was hoping to find some human zombies via parasite. I think my older bro is one cuz he drools when he sees girls at the mall.--Emyn ned (talk) 18:18, 13 March 2009 (UTC)

Surgery
Hi. I've always wondered how surgeons access the brain through the skull, the heart and lungs through the ribcage and the abdominal cavity through the abdominal muscles. Could anyone tell me what happens, ie is the bone just cut away and then somehow replaced later and do you cut through the abdominal muscles? Or if not, how is it done? Thanks. 92.0.253.238 (talk) 20:32, 12 March 2009 (UTC)


 * May I suggest the article on Minimally invasive surgery? It has a good wealth of info and some external links that can answer your question. Livewireo (talk) 20:45, 12 March 2009 (UTC)


 * However, minimally invasive surgery is not available for all procedures. When it's not, in general the idea is to minimize the amount of cutting by cutting between structures and spreading them apart, but yes, bones and muscles are cut as necessary.  For open-heart surgery they the cut the sternum lengthwise and spread open the rib cage, then when they're done they fasten the parts together with wire so the bone will heal.  (Do a web search on "heart surgery" and "sternum".)  --Anonymous, 20:56 UTC, March 12, 2009.


 * [1] for brain surgery, portions of the skull are indeed cut away and later replaced.
 * [2] for chest surgery, the ribs are spread (as Anonymous indicated) with a rib spreader
 * [3] for abdominal surgery, an incision is made and abdominal muscles are pushed to the side. - Nunh-huh 20:59, 12 March 2009 (UTC)


 * (Just a grace note, but don't look too closely into what this entails unless you have a strong stomach. It'll hurt just seeing it.) arimareiji (talk) 21:51, 12 March 2009 (UTC)


 * When you've seen your wife have a Caesarean section - NOTHING like that will surprise you again! SteveBaker (talk) 23:32, 12 March 2009 (UTC)


 * In general, they try to cut with the grain of the muscle fibers rather than against it -- things heal much better and faster that way. --Carnildo (talk) 00:14, 13 March 2009 (UTC)
 * As far as brain surgery: the abdominal muscles are left alone :-) but my neurosurgeon says that a small area of skull was removed when I had to have surgery on the surface of the brain; it was taken away and replaced with titanium plates. Not a large amount of skull is always removed; in my case, the surgeon told me that, if we arranged all the plates together in a rectangle, they still wouldn't cover a normal-sized postage stamp.  Nyttend (talk) 03:59, 13 March 2009 (UTC)


 * And I read once of a child whose skull was malformed; the top of it was taken off, ground to goo and troweled back in place to harden in a less distinctive shape. This account is likely oversimplified. —Tamfang (talk) 07:33, 13 March 2009 (UTC)


 * Katrina Firlick's Another Day in the Frontal Lobe is a very readable account of the work of a brain surgeon. For a lay person, this will tell you as much about modern brain surgery as you ever want (or, hopefully, ever need) to know. Gandalf61 (talk) 10:53, 13 March 2009 (UTC)

Many areas of the brain which commonly have tumors or CSF leaks can be accesses through the nose or mouth. Endoscopic surgery via the nose can access pituitary tumors, for instance, as opposed to opening the skull and damaging brain tissue to get to the tumor. An approach through the mouth and palate can access additional areas. Talk about building ships in bottles! 17:30, 13 March 2009 (UTC)

Orchid Species
I am trying to locate a particular orchid species, but I can't remember the Latin name, and I'm hoping someone here does. The species is unusual in that the plant produces a single, broad leaf. It has a white flower. Unfortunately, I do not know anything else about it and I don't have a photograph. Can anyone tell me the species name?130.127.99.54 (talk) 22:50, 12 March 2009 (UTC)


 * Nevermind; I've answered my own question. It was Nervilia aragoana.130.127.99.54 (talk) 23:00, 12 March 2009 (UTC)

StuRat (talk) 05:22, 13 March 2009 (UTC)

Genetic traits split across continents
I was just watching Andrew Marr's brilliant programme about how Darwin's ideas have had various political effects over the decades, and I missed some deatils about something. He was talking about a recent theory involving DNA and genetics which claimed that a divide in the type of genes that people have can possibly be connected to brain size. The genes thought to relate to smaller brain sizes are dominant in sub-Saharan Africa and larger brain sizes are supposedly linked to the genes from Europe/Asia. He had his own DNA tested and found that he falls into the gene pool common in sub-Saharan Africa. They stressed that although the genetic difference is real, it's relation to brain size is hotly contested. I've no doubt got some of these details a bit wrong but can someone fill me in on what I've missed. Do we have an article on this? And before anyone points out that the page I've linked to gives me the option to 'watch again', I can't do that at the moment. Thanks.91.111.86.221 (talk) 22:51, 12 March 2009 (UTC)


 * We have a brain size article, which references one paper on genetics. We also have Race and intelligence, which is the very definition of "hotly contested". Mimetic Polyalloy (talk) 23:10, 12 March 2009 (UTC)


 * Not having read either article, my kneejerk reaction is say it sounds like an attempt to resurrect some pseudoscientific Nazi eugenics bullshit to me. Astronaut (talk) 23:37, 12 March 2009 (UTC)
 * then maybe you should read the article, shouldn't you. There is a reason that Race and intelligence article and Nazi eugenics are treated as distinct topics. --dab (𒁳) 09:09, 13 March 2009 (UTC)


 * Yeah - they don't sound to be in any way related. Eugenics was (effectively) selective breeding of humans in order to 'improve the species' - which is perhaps a not entirely stupid idea if done right.  Of course the Nazi's didn't do it right - which has gotten eugenics a bad rap - from which it may never recover.  But (for example) if we continue to promote artificial reproductive methods for couples who can't have children for some genetic reason - then we are removing the evolutionary pressure on our species that ensures that we are able to reproduce naturally.  If, in the future, the genes that prevent sufficient sperm production - or which cause kinked up tubes in the ladies - become much more prevalent, then only people with lots of money or comprehensive health insurance will be able to have children.  That is something, I'm sure we all agree is clearly a bad thing - and perhaps a little (and I'm going to use the 'E-word') eugenics may be called for to fix that - limiting the availability of artificial reproductive techniques, for example.  It's not like there aren't tens of thousands of children without parents who would benefit from adoption by childless couples.  That's a far cry from hauling people off to death camps.  Rationally - it's hard to argue against SOME controls here - but the Nazi's have made even the discussion of this somewhat taboo - and I'm sure that what I just wrote is already raising some hackles.


 * The other side of this is the race and intelligence thing. And again, it's not unreasonable to study the impact of genetics on human intelligence - and if in the course of that study, you discover that one "race" (already we're slipping into dangerous territory) - implying some specific mix of genes - has a strong correlation with some measure of intelligence - then that is a valid thing for science to study.  However, the racially-prejudiced nut-jobs out there - and the history of the slave trade (esp. in the USA) have made publishing such studies difficult and (again) almost taboo.  But it's valid science - and the results might turn out to be exceedingly important in understanding what makes us tick.  A correlation between (say) length of middle toe of left foot and intelligence would be an interesting (and perhaps even useful) scientific discovery - but a correlation between skin melamine content and intelligence is likely to cause rioting in the streets.  Although, if the findings were that white males are genetically stupid - then I imagine the results would be widely published (if only by white females - who have long known this)!


 * But there is really no relationship between these two topics UNLESS one uses the results of one's genetic studies on intelligence to push for a eugenic "solution" to improving human intelligence by herding one group of people into death camps. That seems a most unlikely coupling for a rational science-based civilisation (which, of course, we aren't even close to having).  As scientists we'd have to be MUCH more concerned that by tampering with the evolutionary pressures on humanity, we'd do something catastrophic.


 * However, the whole topic is moot because every time one attempts to bring up these perfectly reasonable lines of inquiry - one is immediately stamped as a Nazi (even if you were thinking in terms of limiting future suffering for millions and had no thought of setting up death camps) - or as a white-supremacist (even if your findings are that the Bushmen of the Kalahari are the smartest people on earth and that white guys are the stupidest).


 * SteveBaker (talk) 11:17, 13 March 2009 (UTC)
 * Minor correction. A correlation between skin melamine content and intelligence is not going to concern anyone too much (except, perhaps, consumers of Chinese sourced milk). A correlation between skin melanin content and intelligence would be controversial, however. Rockpock  e  t  00:42, 14 March 2009 (UTC)
 * Oh - you thought I was discussing the horribly non-pc concept of relating skin color to IQ...no, no - it was the milk thing. :-) OK, my bad. SteveBaker (talk) 23:16, 14 March 2009 (UTC)

Thanks. I guess it's my fault for mentioning brain size and race in the same sentence but what I'm looking for is a specific, genuine, recorded, proven difference in DNA that has been discovered (I think). According to the programme, it was just one letter (GTC or A) that was different and it was fairly clear cut that the divide was across Africa.91.111.85.208 (talk) 13:33, 13 March 2009 (UTC)

It's ok, I've found it. It's the work of Bruce Lahn, who apparently states that a gene variant evolved around 6000yrs ago and some of us have the old ancestral type and some of us have the new variant.91.111.85.208 (talk) 13:58, 13 March 2009 (UTC)


 * Regarding race and intelligence, it should be noted that there is a difference between race (read: genetics) and culture (read: learned behavior and values). It is entirely possible that a difference in IQ is the result of culture and not genetics.  The graph found here  shows that Asian Americans have higher IQs than other races in the US.  But is that because Asian Americans really are more intelligent than other races living in the US or that they simply place a greater emphasis on education and as a result score higher on IQ tests?  If the latter, that's a difference in culture, not race.  As someone who lives in the US, it seems as if Asian Americans spend more time studying than other students.  In order to eliminate culture from the equation, you would basically need to take kidnap children at childbirth, raise them identically (which probably means keeping them isolated from the rest of the world lest the world influence their behavior and values) and then perform IQ tests.  Since such an experiment is obviously unethical, there really isn't any accurate way to determine the relationship between race and intelligence.  A Quest For Knowledge (talk) 14:47, 13 March 2009 (UTC)


 * First off, before people get in too much of a huff over this (is it too late?), please do NOT conflate brain size and/or head size with intelligence. They are not interchangeable or even necessarily related.  There are brilliant people with smaller-than-average head size and not-so-brilliant people with larger-than-average head size and everything else in between.  Second, it is inescapeable that genes play a role in the development of bodily structures, including the brain.  We know this because many genetic disorders affect brain development, and can lead to microcephaly or macrocephaly.  In many of these cases, abnormal head size is associated with cognitive deficits, but these are in pathogenic situations, not the normal range of human variation.  Third, there are any number of physical characteristics that differ between various geographic groups in the world -- why not head size or brain size?  If there is a clear association between a gene that is more prevalent in one population than another, that correlates with differences in a given physical characteristic between populations, and has a biological function that supports the conclusions drawn by the association study (as is the case for microcephalin) then why should this information be problematic?  The problem comes in people ascribing undue importance to the genetic and physical differences.
 * On the other hand, the controversy over a genetic contribution to "intelligence" is a completely different subject. There is an intense discussion about this going on in the journal Nature right now  that really sets out two sides of the discussion.  Recommended reading before we continue what is an inherently visceral argument. --- Medical geneticist (talk) 14:53, 13 March 2009 (UTC)
 * I've got 'em. Email me if you want copies (not you MG, you obviously already have them). They are good stuff. Franamax (talk) 23:34, 14 March 2009 (UTC)
 * Yes, indeed. And it's definitely not helped by the fact that there is no solid definition or test for intelligence.  IQ tests really only measure how good you are at IQ tests and there enough cultural biasses in them to make testing of people of widely different cultural backgrounds an exceedingly touchy matter.  Unless the differences are enormous, there are any number of experimental slip-ups that could annihilate the very small differences that are claimed in what few studies have been done. SteveBaker (talk) 22:49, 13 March 2009 (UTC)