Because the imperialists bogart all the cool stuff.
Because people who make them know what sells.
Speaking of gratitude, my employer's volunteer coordinator just sent around a solicitation for people to help low income families with their taxes. I'd rather by whole house was filled macramé shit made by Guatemalan peasants.
I'm sure the help is needed, but I'd rather we just paint stuff again.
To be earnest about it, it's not entirely true. Ten Thousand Villages
and Novica, par example, both have a lot of beautiful (and some dorky) stuff. My problem with a lot of it is that it's purely decorative, which is the last thing my cluttered house needs.
But there are also fair trade clothes and coffee and chocolate, even soccer balls. I've gotten some awesome p.j.'s and baby clothes from Global Mamas. I mean, cute, right? Come to think of it, this would be a great dress for you.
And by "you," I mean Moby, obviously.
The stuff has to be a bit crappy. They are $40 for a man's shirt. A good shirt is going to cost more than that even if you exploit the people making it.
I should probably stop mocking charitiable organizations as it hurts my grammar.
Just pre-emptively: Racist.
Also, I recall fondly the little carved wooden animals that liberal American churches sold to support people in the Third World. I wonder where my menagerie of them ended up.
Ten Thousand Villages has some attractive planters, but I don't really go out of my way to a special store for planters. I either get them at the garden store when I'm there or get plain terra cotta ones at the hardware store.
Those turned into olive wood Nativity sets. Too bad the Palestinians weren't oppressed into sculptors.
To counteract the laissez-faire of 2, there could be a market failure if even considering making fair trade products is something only the dorkiest (in the OP sense of the word, which I don't really get) entrepreneurs do in the first place.
Too bad you can't buy a fair trade X-Box.
Cottage industry trivia: according to the Amsterdam Resistance Museum, towards the end of WWII, when over a hundred thousand Dutch were living in hiding, and the Resistance was getting huge, the hiders were organized into making greeting cards and other kitsch, the proceeds going to the Resistance coffers.
This is one of those times when I don't know what you mean by dorky. Ornamental? Kitschy? Useless?
I tend to buy chocolate, coffee, clothes, purses, and notebooks. I also tend not to give a lot of gifts.
Giving gifts is fun and should be encouraged. Just because decades of dreary family Christmases have robbed the moment of charm and the Style sections of newspapers make it a chore doesn't mean we should abandon it.
Those turned into olive wood Nativity sets.
I received one of these from my mother!
20-inspired: One of my coworkers just mentioned that she's buying gifts for her children's teachers. Having never had children in school at a holiday before, I hadn't thought about this and really, really don't want to do it since I still have to buy for the actual kids. Am I being horribly tacky and culturally inappropriate if I don't do anything for the minimum of seven teachers I deal with this year? Ugh!
23-inspired: Are gifts (or tips?) to mail carriers normal and expected? We never do this, and our postal service is really not very good--mail doesn't come every day, mis-delivery is not at all uncommon, and if we leave something sticking out of the box to be picked up it is generally ignored. This makes me less inclined to give/tip/thank the mail carrier at the end of the year (something I'm only vaguely aware of people doing at all, though I may just be clueless on the subject), but also makes me wonder if we get crappy service because we are cheapskates.
I don't think so. If Mara really likes some of the teachers, you could ask her if she wants to make cards. Or you could write a note to any of them that have been especially helpful with the girls if you're inclined and can find the time. But I don't think you have to do anything, and certainly not for 7 teachers.
23: I think most schools actually forbid it. If the kids want to make cards or something, I'm sure they'd be appreciated, but I wouldn't sweat it at all.
(I have slipped teachers Staples gift cards, assuming they were getting stuck buying supplies for their classrooms, but that's not really a present, more of a subsidy, and isn't something you should worry about unless you're feeling guiltily affluent.)
24: We tip the mail carrier, but Buck runs a mail-heavy business out of our home -- if checks from advertisers went astray, he would be sad. I'm not sure how standard it is.
We tip the mail carrier and our postal service is still terrible. But we do it anyway.
26: Mara's school sticks to very secularized versions of the holidays, but Val and Alex are both in Santa-heavy public schools (two different schools for Alex, which is part of where the numbers start adding up) that are having "holiday" parties with Christmas trees, etc. The idea of buying them gifts hadn't even crossed my mind, so I guess if I look tacky I can look tacky. I'm already planning to talk to Val's principal about the extent of explicit Christmas stuff in the curriculum and wtf, so I might as well keep the Scrooge thing going.
I've just been so overwhelmed and have no idea what I'm doing. I won't be getting any Christmas presents as Lee and I don't exchange and my mom may give me something from Big Lots but nothing more since I'm not a Christian and not a child. But I feel I have to spend all kinds of money so the kids have presents and so they also have little presents to give to their siblings and so on. I think I'll take them to a paint-your-own-pottery ripoff place so they can make something for their parents. I'm so sick of supervising artsy crafty stuff. Not in a good emotional place as a parent of littles today.
24: I doubt it affects your mail service. I think it falls in the category of nice but not expected. (I do think it was more common back in the days when women were sensible enough to have their kids at 20 and were home during the day.) In any case, cash tips are banned by the USPS and gifts are supposed to be worth no more than $20.
At the ages your three are at, you can make them perfectly happy with some very minimal plastic crap from a dollar store. And honestly, I wouldn't sweat faking presents from them either to each other or to their parents -- if you were into it, it might be nice, but it's not the sort of gesture anyone sane will miss.
Little plastic dishes, random toy trucks -- anything cheap and bright-colored will make a preschooler as happy as anything else.
Gifts to public school kindergartner teachers are very common (I can attest to this as the daughter of one). Common, but certainly not necessary and occasionally just a pin. Though, I always liked getting to open all the 'extra' presents on Christmas morning!
Seriously, if you're running out of energy, this is not the place to spend it. Bake cookies with them or something if you want to, but really don't worry about buying presents. Something for each of them, sure, but it doesn't have to be expensive or thoughtfully chosen.
29: I thought Val & Alex weren't staying with you any longer which is why I didn't mention them, but same goes for them and handmade cards, obvs.
pain! not pin! Though I am sure some pins have been given. The most common gifts are often useless knick-knacks and nearly all of them include apples. The most appreciated ones that cost money are gift cards, but hand-made cards and little things like that go over best.
31: Yeah, Mara's getting a new dress for her favorite doll and a doll that can go in the bath. Alex requested a plastic farm, so probably that and maybe some building stuff. Val will get an art kit she can use without supervision. Each of the three will get one of the stupid Zooble toys so they stop monopolizing Val's and making each other mad, although obviously this plan will backfire. A book or two apiece, and anything beyond that will be little silly stuff they'll like most.
I do think we're going to be expected to do fake presents from them to the siblings who don't live with them, but that basically means I'm doing the same thing as people who get presents for all the kids in a low-income family who otherwise wouldn't get much, so I'm okay with that. I'm just not going to be able to buy for all Mara's cousins who live with her siblings, in part because I don't know their names yet. I'll figure something out, though.
Also, my commentary is not meant to indicate that Thorn should get the teachers anything. Definitely don't worry about that.
34: Val and Alex are with us until January or February, probably. Lee relented and is being pleasant to them, especially after watching Precious this weekend and having some kind of internal come-to-Jesus moment.
Last year, I did all my shopping at Ten Thousand Villages and everything was well thought-out and so on. This year, it's going to big chain stores and all done in one afternoon, probably. Regardless or what our family's like next year, I should swing back to dorkiness as the norm.
37: Yeah, I was thinking that I'd get something for the teachers when Val and Alex transition from our home and they're no longer "my" teachers anymore. Maybe if I didn't hate the director of Alex's program so much, I'd be more positive about this.
Oh, presents to other siblings they don't live with is nice. But again, random cheap shit is fine -- the kick of Christmas is mostly about having packages to rip open, not that the presents themselves are awesome.
41: Her 3-year-old brother is obsessed with marbles, and apparently that's a craze throughout the housing project where they live. I find that so totally adorable! So he's getting more marbles in a cute crocheted marble bag. Beyond that, fairly generic stuff. I barely know the siblings, though I hope to eventually.
||
I love it when my job becomes all about rumor-mongering.
|>
Can you explain to me why it's easier to rule out Higgs with mass lower than something *or* higher than something, but not in the middle? Naively I would have expected that searching would get harder is it got heavier and so you'd only have a range ruled out below some mass.
a whopping five inverse femtobarns of data
What's the conversion factor between a femtobarn and a shitload?
So what are they actually finding, or is it far too soon to know?
What are the options if there is no Higgs Boson?
The rumor I heard is evidence of a Higgs boson with mass 125-126 GeV.
Am I still safe assuming the FTL neutrino thing was the result of some experimental flaw?
Yes.
43: The Higgs boson will be found at a mass of 223 gigaelectronvolts. They missed it because it was hiding behind a bag of chips.
What if they just told everyone they'd found the Higgs boson, even if they hadn't? Then all these physicists could get on with their lives.
47: Cole slaw or a salad, but the salad is $1.50 extra.
48: Yes. The trouble is trying to pin down whether it's both experiments, in which case it would be very convincing, or just one.
44: A heavier Higgs decays in more spectacular ways that are easier to tell apart from all the other stuff the collider makes. A lighter Higgs is easier to make but decays in messy ways that are hard to disentangle from background. The limit at low masses comes from older experiments where the backgrounds were different and the lighter Higgs was more distinctive. The LHC is mostly setting limits on relatively heavy Higgses, and working its way down.
Finding the Higgs boson at a mass of 476 GeV or more is considered highly unlikely.
Does this mean that they think it's highly unlikely that it would have that large a mass, or that if it did they wouldn't be able to find it?
I read right over ()'s pin/pain mixup, because my schoolteacher mother did indeed get lots of pins as gifts. Apples, mini chalkboards, ABCs, more apples. Stuff just made to go on the denim jumper they issue with an elementary ed degree.
(Note: I do realize that elementary teachers do not necessarily dress like that.)
56: Nifty, that makes sense.
So far the way it has worked in our school is that the room parent takes up a collection among all the other parents to buy a gift card or something for the teacher. A standard donation from a mom is $5, a large donation is $10. Last year when I did this for my kindergartner many parents donated, but it's a wealthy district with lots of parental involvement in general.
Regardless, don't feel bad if you don't have time or if you just give a home made construction paper card. Honestly, I think the teachers like the home made cards best. Or maybe also treats.
58: I think there would have been more pins if it had been my mother rather than my step-father!
Also, one of the really neat programs his school instituted was subbing out the traditional, often unwanted holiday gift with saying a) there is no need to give presents but b) if you really want to, you can get these much needed school supplies for the classroom. It meant that those parents who really felt the need to get something (to make a stereotyping generalization, often immigrant families from places where teachers were traditionally given more respect than in the US) were able to, and the teachers got something they could actually use and could stop spending their own money on such things. (A sad commentary on the state of school funding, of course.)
Bottles of Cristal and Grey Goose are always appreciated.
MH:
I'll put you on my mother's Christmas present list. Over the years she has single-handedly kept the women in about 3 Mayan villages in full-time employment.
Last year (for my December birthday) she sent me: a hackey sack (is it 1997? how did she even find this?) and some impractically-sized cloth zipped bags w/out straps made by Mayan women, a marzipan pig, and about 10 different cheese-cutting utensils (made by exploited Norwegians), a plastic hedgehog-shaped vegetable brush, and a set of Swedish flags.
a marzipan pig
But those are awesome! I'm eating one right now (really!).
63.1: Only if the Mayans were right about the world ending.
[M]ade by exploited Norwegians....
Life in a wealthy petro-state can be difficult.
24: Are gifts (or tips?) to mail carriers normal and expected?
My father was a mail carrier after he retired from the military -- I wouldn't say gifts are normal and expected, but he was really pleased by them. But then, he walked a regular route for years, and paid attention to whether old Mrs. Jones and Mr. Smith were receiving their social security checks on time, soothing them (as they met him at the mail box) if the check wasn't here, and so on. So if Mrs. Jones gave him a small box of homemade fudge for the holidays, he was quite bashfully gratified. He didn't mind the occasional gift of booze, either.
I tend to think gifting mail carriers and teachers is a community-building thing: often -- not always -- these individuals, as public servants, take their work (and their clients, whether people on the mail route or "their" kids in the class) seriously and personally, and some individualized appreciation of the part they play in the community is a good thing.
Several years ago I had a marvelous conversation with our home mail carrier, who had after all noticed that he was delivering The Nation to my mailbox weekly (back when I subscribed), about Howard Dean's campaign. He was a fan of Dean! What did I think? I was completely surprised and charmed by his enthusiastic and knowledgeable introduction of this topic, and did start leaving him some small chocolates at holiday time. Figure he might have some kids or a sweetheart at home who'd like to share them.
None of this is required, of course; it's just the community-building thing.
Wow, that was longer than I thought it was.
Jesus. Andrew Sullivan and Ta-Nehisi Coates have been having some kind of deeply frown worthy exchange over Sullivan's idiotic race and IQ post? I just jumped into it here and am half-heartedly working my way backward.
Edit "frown worthy" above to "cringe-worthy", actually. The two of them appear to have decided to stop talking about it.
This is one of those times when I don't know what you mean by dorky. Ornamental? Kitschy? Useless?
No...tiresomely repetitive? And just kind of health food crunchy granola style? There's plenty of stuff made by indigenous people that's beautiful, and some of it even makes it to rich people in other countries, but somehow at these little bazaar things like was held at Heebie U the other day, all you get is stuff intended for rich people in other countries, and most of it is kind of dorky.
I did buy a small beaded pouch, and two onyx bowls, and some jellies and chutneys, and some almonds, to give as gifts. But still.
parsi, that's (68) a sweet anecdote all around
Thanks. On a reread I feared I was lecturing or earnest or gushing. At any rate, I reminded myself to give my mail carrier something this year. He's pretty cool, and last year I think we just re-gifted him a chocolate orange someone had given me (which, I hate those things) - but that's a pretty lame gift. Since chocolate oranges are gross.
What if they just told everyone they'd found the Higgs boson, even if they hadn't?
The jig is up, essear.
Since chocolate oranges are gross.
Madness.
75: There's a site that you can find by prepending the letters "sn" to "arxiv.org" (sorry for the awkward google proofing) that randomly generates paper titles and abstracts, much in the manner of that strip, and sometimes they're surprisingly hard to distinguish from normal abstracts on arxiv.org.
Er, what's exactly wrong about that?
Can I just assume that subatomic particles don't have mass and therefore I can eat all I want?
79: because the UFC is going to announce the Biggs hoson. Duh.
78,79: is what's wrong that the existence of the Higgs Boson at whatever energy level will basically confirm the standard model? Because if so, I totally guessed that.
Or maybe just that that energy is bad for supersymmetry rather than good?
82, 83: Yeah. Any energy is compatible with the Standard Model, more or less. Lower energies are more compatible with supersymmetry. What they're (possibly) seeing, 126 GeV, is heavy enough that it's in some tension with supersymmetry, or at least with minimal versions thereof. This is scaring the shit out of all of us, basically, because if there really isn't anything there but the Standard Model then the field is gonna get real boring real fast. It's too early to be too worried about that, but this is not the outcome we've been hoping for.
Do I understand right that the worry isn't that the standard model fully captures physics, but rather that new phenomena outside the standard model might not happen at energies low enough for us to run experiments?
84: Have you considered transportation planning?
86: He presumably wants something less boring.
Oh. I thought he wanted a problem without a solution.
85: Yeah, it's entirely conceivable that the Standard Model describes energies up to absurdly high scales that we'll never probe. Most of us don't really believe that will be the case, because the SM alone is weird; it doesn't contain a mechanism explaining why the Higgs mass is what it is, and it's fine-tuned, in the sense that a tiny change in the parameters of the theory would lead to drastically different values of the physical masses we see. But that's a dangerously tenuous argument; nature doesn't have to be something we're comfortable with, and we could live in a world that looks fine-tuned for reasons we don't understand. So we're all a little nervous that maybe the SM is just it, as far as things we can hope to experimentally probe go. (We know there's more out there, like dark matter, but there's no guarantee that dark matter has to interact with us in any way other than gravity, in which case we would never learn any more about it, either.)
I just got some stuff from a Ugandan organization called Awava (http://www.awavamarket.com/home) and it is fair trade post-conflict income generating unicorns and rainbows etc. and pretty good-looking - the yoga mat bags are particularly inspired.
I give my postie money at Christmas. In the past there have been two of them, a normal post person and a parcel man, but this year they seem to have merged into one new man. So yeah, I'll give him some cash in a card. He's a good postman.
I always wonder about the dustmen. One year I left a case of lager out and figured they could share out the bottles.
The word "dustmen" makes me expect to start hearing about chimney-sweeps and scullions next.
We use to have a great postman who gave our dog treats and was charming (AB says she didn't like him that
But then he got transferred, and the new carrier hates our (very sweet) dog, delivers so late in the day that I can't actually deposit checks the day I receive them, and is generally unpleasant. No soup for her (actually, she's grown faintly more pleasant, but it's taken her like 3 years to stop being outright surly; should we engage in positive reinforcement?).
I outright bribed the garage guys to haul off demolition materials this summer; should I follow that up with a little something for the holidays?
RE: teachers, AB has always given gift cards to bookstores, but now there are no bookstores in the city. I guess you can use them online - I hate to give a gift that requires someone to drive to a mall.
Iris was so enamored of her teacher this year that she spent much of Sept. concocting little gifts and cards for her - she even made a "brooch" out of a safety pin and ribbons and beads. At our parent-teacher conf, teacher said that the best thing we could do would be to put in a special word for her with the principal: it's her first year at the school, and she really wants to stay. We need one of those Heifer Int'l. cards that says "This Christmas, a heartfelt recommendation was given to the principal on your behalf".
Hmm. HTML fail in 94?
+ way, but she does gush about his dry wit) and one year saved our bacon by bringing back the tax envelope I had unbelievably failed to stamp, letting me stamp it, and ensuring it got back-postmarked to 4/15. He certainly got a card and cash at Xmas.
I reiterate my suggestion that essear work on protein folding (because I am devoid of new ideas).
I wonder if there's any good review article on protein folding aimed at people with a physics-y bent. I've always been confused about whether one should expect the problem to be solvable in principle (let alone in practice), which might mean I'm confused about what the problem even is.
Skimming this clarifies a few things; e.g., apparently biological proteins are different from random polypeptides in that they have relatively few different possible conformations. Looks like it might be worth reading the whole thing.
99: That's pretty much the extent of my knowledge (which was in high school, so I might not have known even that much). But the guy who taught my mechanics class in college was working on the problem, although I have no idea what he's been doing since then. I think he was a postdoc at the time.
Also, I read something recently that scientists have discovered there's a little box in the cell, a wardrobe of sorts for proteins, that helps proteins fold themselves by giving them a quiet space away from everything else. I thought that was pretty cool. (Also, probably butchering the science.)
Proteins do not always fold into their lowest energy conformation.
105: Yeah, that's what's confused me when I've heard a physicist talk about the problem before. If it's really hard for you to calculate the ground state because there are lots of other metastable local minima, then probably some of those are relevant in biology too....
106: but having all the ground states isn't terribly relevant if you don't know which ones are important, right?
Er rather it doesn't seem terribly efficient to search the whole landscape for minima if only a small percentage of them are important.
... aaand looking at the wikipedia page for protein folding, I'm for sure misunderstanding something.
Kobe! Or maybe I misunderstand something.
Physically, thinking of landscapes in terms of visualizable potential or total energy surfaces simply with maxima, saddle points, minima, and funnels, rather like geographic landscapes, is perhaps a little misleading. The relevant description is really a highly dimensional phase space in which manifolds might take a variety of more complicated topological forms
Thank you, wikipedia. That's not a bit helpful.
107: Yeah, that's why I'm confused about what the problem is and whether it's tractable. One, possibly just stupid, physicist I heard give a talk on it once implied that the challenge is to find the lowest energy state, which doesn't seem very relevant for biology, since real proteins might not be in that state. Probably other people working on it are doing more sensible things. Maybe if I get around to reading more I'll know what I'm talking about. It just seems to me like it could be very contingent on the environment where the protein forms, what enzymes are floating around, and other stuff that's hard to use as input in a physics problem.
I like how biologists openly call things dogmas.
112: It's just scientific journalism, but this nicely makes the case that protein folding is very much influenced by surrounding conditions.
Thank you, wikipedia. That's not a bit helpful.
It's funny how sometimes Wikipedia totally fails at its basic job. I just had a call from a friend who's hired an architect for a (big, out of my league) job. She needed to know about a specific drafting program and associated technology. Even though she understood the basics, the relevant wiki article was so poorly written that she bailed and just asked me.
On one level, it's surprising that any wiki articles are useful, but we've grown accustomed to it being functional for your basic "elevator pitch"-style intro to topics, and so complete failures like this article catch us out.
I don't know much about protein folding, but I know that for a lot of proteins, especially the ones with hydrophobic sections that lead to them being embedded in membranes, the folding doesn't work unless it is done in the presence of certain other proteins called "chaperones". For example, Gp96 is needed for Toll-like receptors to take their proper configuration. Misfolded or unfolded proteins form aggregates that can get in the way and lead to cell death.
Don't know what 104 is referring to, but it sounds interesting. Most proteins are produced by ribosomes attached to the endoplasmic reticulum, and they end up in the ER and get folded there. The ones produced by free-floating ribosomes that go directly into the cytoplasm are presumably less complex and need less folding. Never thought of that before.
Obviously all proteins end up "folding" into their configuration, whether independently or with help. I guess some need chaperones because otherwise they would get stuck in an intermediate state that happens to be an low-energy state, instead of pushing through to reach their final form (which is also a low-energy state).
104 is in reference to the article in 114; I was being lazy earlier!
The tower of paper behind that guy is terrifying.
Hah. I didn't even notice it; I think I've been in too many professor's offices that resembled it!
You guys know about the protein folding game thing, I am sure? Here's a link to Foldit. Profuse apologies if I originally read about all this here.
If the thread isn't completely dead and people would like, I can hold forth on protein folding.
112.last definitely gets it right, not that the physics types who swoop in to solve all of biology's tough quantitative problems would admit it. Don't be one of those guys, essear.
I do fine folding flat proteins, but the fitted ones come out looking worse than if I'd just crushed them into a ball.
I can't even swoop in and solve my own problems.
But yes, please do hold forth!
Okay then, will do. Give me a minute; this will take some time to write properly.
Also, I haven't kept up with the literature in the last seven or eight years, but if there are particular recent results that you're interested in I can take a look and try to help clarify things.
I was able to pwn 125 because I've had my echolalia treated.
This thread seems to have drifted into part of what my lab works on. Who knew that Unfogged was full of protein folders?
I thought it was 95% lawyers, 2.5% mathematicians and 2.5% armchair revolutionaries.
There has always been social science and humanities peoples.
Way more than 2.5%, assuming those are armchair revolutionaries.
I'm not a science person, beyond a brief background in undergrad (and some work in the history of science). I just think it's fun! Tell us more, AcademicLurker and Gabardine Bathyscape.
When I first showed up here, it was part of my general reaction to the political blogosphere: "Who knew there were this many philosophers in the world?" (Counting anyone who'd done any graduate work toward a philosophy degree, or anyone who talked about undergraduate philosophy, as such.) I don't think I'd ever run into someone who'd seriously studied philosophy before.
It used to be full of philosophers; not so much any more; now it's mostly lawyers; but I whined about that before.
Protein-folders, carry on!
I deliberately refrained from #127. Anti-pwn.
In recompense, I won't make the obvious joke about 137.2.
Goddammit. I am trying so hard to give you all a lovingly rendered ASCII-art picture of the protein backbone, but neither <tt> nor <pre> tags will give me a fixed-width font, and line-initial spaces keep getting eaten. Help?
You can type a lot to make spaces but it's a pain any still may not do what you want.
Some of us are more like ex-philosophers. Although I still have the sekrit hat.
Thanks, fa.
Right. Backtracking slightly to make sure everyone is on the same page: The thing you always have to keep in mind with biochemistry is that we're at the mercy of Brownian motion. Everything in the running of the cell depends on molecules doing the right thing when they bump into each other. When molecule A hits molecule B, are there sparks? Do they spoon? Do they have elbows in all the wrong places? Does B find A offputtingly unctuous? Will either of them ever be the same again?
Part of the reason biology is rife with anthropomorphism is that it's rather terrifying to realize that the molecules that keep us alive have absolutely no sense of mission. What they do in any intermolecular collision is entirely dictated by the structures of the things that collide: in the usual three dimensions, plus the patterns of charge and hydrophobicity that decorate their surfaces. (Plus some other stuff, but let's skip that for now.) So when the cell builds molecules, it has to not only use the right bonds to join up the right collections of atoms, but also get the whole hot mess into the right configuration.
Many of the molecules the cell builds are reasonably well-behaved. Metabolites tend to be quite small, so they just don't have a lot of options for long-range structure. Lipids tend to be either very very constrained (like cholesterol; four conjoined rings, not going anywhere) or very very floppy (like the long-tail fatty acids in cell membranes, for which conformational flexibility is half the point). Proteins, though—proteins are a problem.
A small protein might consist of a chain of 100 amino acids, joined end to end. Since each amino acid contributes three atoms (the amine nitrogen, alpha carbon, and carbonyl carbon) to the protein's backbone, that's a chain with 300 links—300 covalent bonds. Covalent bonds permit some degree of flexibility in the bond itself, plus some degree of rotational freedom about the bond axis; single bonds have the most freedom, and bonds of higher degree are progressively more constrained. In the protein backbone, two out of every three bonds are single bonds; the third of each triad, the bonds that join the carbonyl carbon of amino acid i to the amine nitrogen of amino acid i+1, behave somewhat like double bonds, with relatively fixed geometry. (These more fixed bonds are the peptide bonds, which may ring a bell; they're the ones whose formation the ribosome catalyzes during protein synthesis.) ASCIIfied, and ignoring substituents, the protein backbone looks a bit like this:
Ca- C C = N
/ \\ / \
...N N - Ca Ca- C...
That's three amino acids' worth; the bonds shown with two lines are the peptide bonds, the more fixed bonds. Rotation about the other bonds means that that nice flat backbone can come popping out of the plane of the screen. Imagine this: treat the whole molecule as fixed, except for the first Ca-C bond. Now spin the right half of the molecule around that bond axis: the N-Ca and Ca-C links from the bottom row come up and out of the screen, then farther up and back into the screen, then down and back behind the screen, then back to their starting position. Now, most of that 360-degree sweep is unstable—the bits of the molecule that I haven't drawn, the hydrogens and side-chain atoms and whatnot, will be too close for comfort in all but about three spots. Still, that's three possible configurations just from rotation about one bond. Move down the line to the C=N bond: not much flexibility there, that's the peptide bond. Move down the line to the N-Ca bond: this is just as flexible as the Ca-C bond, and again, if you imagine the right half of the molecule spinning about the axis of this bond, there are three permitted states. All this flexibility compounds rapidly. Each peptide bond is flanked by bonds that can exist in any of three states: the backbone of a protein of 100 amino acids and 99 peptide bonds has 198 bonds that can exist in each of three states, so that's 3198 possible configurations. At perhaps a femtosecond to explore each configuration, it would take far, far longer than the lifetime of the universe to fold into the one right configuration (the "native state"). And that's for a small protein.
This is the not-actually-paradoxical Levinthal paradox: protein folding actually happens on microsecond timescales. That means protein folding can't be a purely random walk through backbone-conformation space. The question is, what guides it? Some proteins will fold correctly in isolation, just one protein in a buffer solution, so all the necessary information has to be contained in the protein itself, in the sequence of the sidechains that distinguish one amino acid from another. If that's the case, if amino acid sequence dictates structure, it ought to be possible to look at a given protein's amino acid sequence and predict how it will fold. We can't. That's the protein-folding problem.
(Stay tuned.)
Put it on pastebin and link it here?
Thanks, GB! That was totally fascinating. If you self-edited in the interest of length, feel free to spout some more.
Is it the type of thing where smart people suspect there's an extra factor affecting things that no one has put their finger on yet? Or is it the type of thing that people believe they actually do understand it at the current time, but finding the answer requires armies of computing power to make a dent any specific case?
I self-truncated in the interest of eating some lunch, but will continue spouting.
People do think that this will be solved, possibly in the next decade. We understand a lot more than we used to, and computers are getting faster. Not there yet, though.
It's at least plausible that we won't be able to solve it using ordinary computers, and will need quantum computers.
Have you tried using Excel to do the calculations?
Sometimes having that formula-making paperclip really makes the difference.
The link to Foldit in 122 is wrong; here's the real link. I'd be interested to hear any impressions of it that the resident protein-folding experts have.
I'm glad to have made the offhand comment that sparked this subthread, but I have a deadline to make tonight so I'll have to check in later.
Huzzah for 143.
I really enjoyed HS- (and AP-) level bio (and chem), but I could sense that it would really rapidly get beyond my comprehension/patience. But I really love this level of explanation.
To continue: about those side-chains. Nearly all proteins draw from a set of 20 amino acids that differ from each other only in the collection of atoms that dangle off the alpha carbon. In the simplest amino acid, glycine, the side-chain is just one hydrogen atom; in the biggest, tryptophan, it's a two-ring system. There's a lot of scope for different chemistry here. There are large and small, acidic and basic, polar and hydrophobic, flexible and constrained side-chains, and nearly all proteins will have a healthy mix of the various chemistries. When a protein chain begins to fold, the acidic side-chains can form stabilizing ionic interactions with the basic side-chains; the flexible side-chains can help the backbone negotiate tight turns; the polar side-chains can form networks of hydrogen bonds; the hydrophobic side-chains can give folding an entropic boost by packing together, freeing the ordered shell of water molecules that otherwise shields them from solution. The backbone can contribute too; hydrogen bonding between backbone carbonyls and amino groups underpins two major motifs in short-range structure, the alpha helix and the beta sheet. All of these interactions contribute to the stability of the folded protein, and all these contributions are necessary to compensate for the massive loss of entropy inherent in getting from 3198 states to one.
It's easy to rationalize a known protein structure in these terms: oh, I see, there's this salt bridge over here, and this hydrogen bond network here, and really nicely packed greasy bits here. The difficulty is that the native state is typically only a little more stable than the unfolded protein, and frequently has a very slight edge on alternate folds. This is where the talk about energy landscapes comes in. Conformation space has twice as many dimensions as a given protein has peptide bonds: one dimension for each freely rotating backbone bond. Imagine we can project all these dimensions onto just two, x and y, and make free energy the z dimension. Every (x,y) position will permit some combination of potentially stabilizing interactions, giving that position a particular free energy. More stable things have lower free energy, so (with some interesting exceptions) the native state is typically the global minimum, the lowest point on this landscape. For some proteins, it's that easy; the landscape is basically smooth, with few or no other local minima to trap a protein en route to the global min. For others, the landscape is rugged, and it's very unlikely that a nascent protein will find its native state unassisted.
As essear said above, context is really key for protein folding. Because the native state is only marginally stable, small perturbations to the thermal and chemical environment can be enough to throw the whole process off. But other large molecules in the neighborhood also matter. Hydrophobic interactions are quite non-specific, and many correctly folded proteins have exposed hydrophobic patches. Say we have a nascent protein, not yet folded, in whose native state hydrophobic residue X will be buried deep in the protein core, nestled among other greasy bits. But X doesn't know that, and there's nothing stopping it from just glomming onto an exposed hydrophobic patch in a nearby protein. Now we've got a mess: it's hard enough getting the right set of interactions to form when we've only got our nascent protein's side-chains to worry about, and now all the surface-exposed side-chains of the passerby protein have been thrown into the mix as well. Disaster.
(Stay tuned.)
Disaster.
Does that mean mad cow disease or the like?
and now all the surface-exposed side-chains of the passerby protein have been thrown into the mix as well. Disaster.
Now I'm paralyzed with fear that my proteins will fold incorrectly.
It's a damn good thing that God is watching over this shit. There are so many things that could go wrong. You're walking down the street, and suddenly a bunch of key proteins will fold wrong, and BOOM! There you are twitching on the sidewalk.
All denatured like a hard-boiled egg.
To continue: That sort of interprotein glomming is disastrous not only for the nascent protein but also for the protein it glommed onto: that protein is now covered with goo, and it won't be able to interact properly with other players in the cell, AND the goo may keep recruiting other molecules and sequestering them too. We're worse off than if the nascent protein had never been made.
And yet: we're alive! So the cell must have some coping strategies, ways to prevent this sort of mess or to clean it up when it does happen.
Strategy one: co-translational folding. Proteins are synthesized from one end (call it the old end) to the other, and the chemistry happens deep within the ribosome. The way out into solution is a longish pore called the exit tunnel, and the old end of a nascent protein gets nudged away down the tunnel toward solution as amino acids get added to the new end. Neat thing: the exit tunnel is just big enough in cross-section to permit the nascent protein to form an alpha helix, one of the structural motifs I mentioned above. So (for some protein folds; they don't all rely on helices) there's a chance to lay the groundwork for the native state, with minimal confusion from long-range intramolecular interactions and essentially no interference from other molecules. If what comes out of the exit tunnel behaves as a string of a few alpha helices rather than as a string of a few hundred amino acids, the number of possible conformations is much, much smaller, and the right conformation is much, much easier to find.
Strategy two: translational pausing. This is almost impossibly cool*. I said above that we've got a palette of 20 amino acids, and you probably know that the genetic code is read by threes: three nucleotides, a codon, encode one amino acid. But given that there are four distinct nucleotides, there are of course 43=64 possible codons. Three of the 64 mean STOP, but that leaves 61 to cover the 20 amino acids. That is, a given amino acid can be encoded by any of (on average) three codons. Cast your mind back to high-school bio and remember that tRNA acts as the adaptor between messenger RNA and protein: each tRNA carries both an anticodon (the complement to a particular codon) and the amino acid that codon calls for. If you've got 61 codons coding for amino acids, you need 61 tRNAs. Now, some amino acids are more common than others; of course you make more of the tRNAs for common amino acids than you do for the rare ones. The fantastic thing is that there's also variation in the frequency of the different codons used for a given amino acid, and in the levels of the corresponding tRNAs. Makes sense, right? If 75% of the time you want glycine you call for it using the GGA codon**, you want the large majority of your glycine tRNAs to have the TCC anticodon.
Say you need to add glycine at position 50 of a nascent protein. If the messenger RNA uses GGA, it won't take long for the correspondingly common TCC tRNA to blunder in and deliver its glycine. Translation carries smoothly along. If the mRNA uses a rare glycine codon, it will take longer to find the correspondingly rare tRNA, and translation will pause. Now, translational pausing can be quite bad; you don't want to have all your ribosomes tied up in unproductive complexes. But it can make all the difference to folding. The longer the piece of protein that needs to fold, the larger conformation space is, and the less likely a random walk to the right conformation will be. Remember that the nascent protein is emerging from the ribosome a little at a time: conformation space is getting steadily larger. Translational pausing offers a chance for folding to catch up, for local and mid-range interactions to form while conformation space is still relatively small. When everything is tuned just right, that happens on about the same timescale as finding the rare tRNA so that translation can proceed.
Strategy three: chaperones. These are the subject of the NYT article Paren linked above. I'm definitely out of date on the literature here, but the general idea is much like giving an overstimulated toddler a timeout. Chaperone complexes (or at least the GroEL/GroES system) are big protein vaults that can be opened or closed by hydrolyzing ATP. They trawl the cell with the vault open, and because the insides of the vault are hydrophobic, they pick up things with lots of exposed hydrophobic patches. (A few exposed hydrophobic things are fine, but the more a protein has, the more likely it is to be misfolded.) When they pick something up, they burn an ATP to seal the vault. And because they are awesome, the conformational change that seals the end of the vault also flips the vault's insides from a state with exposed hydrophobic things to a state with exposed hydrophilic things. Suddenly the vault is a very uncomfortable place for an unfolded protein to be: it becomes far, far more favorable for the protein to get all its hydrophobic bits buried in its own core. The seal on the vault has a timing circuit (also awesome), so after a little while it clicks open again, and that change flips the walls of the vault back to hydrophobicity. Now the vault is an uncomfortable place for the newly folded protein, and it stumbles back out into the cell. (Of course, sometimes one vault cycle isn't long enough to permit folding; that's fine, the unfolded protein will be sticky with respect to the open vault's walls, so it will stay put for another cycle, and another, etc.) This seems like an expensive strategy, what with all the ATP burning, but that ATP budget is nothing compared to the amount of energy that's already been sunk in making the protein.
I bet other people here know much more than I do about current strategies for tackling the folding problem computationally, but my impression is that the smart money is on D@vid B@ker at UW. For what that's worth.
*And not just for these reasons. There's a lot of really neat research in this area right now.
**I am making this up: this is a glycine codon, but I have no idea how common it is
Many years ago, I read a book about Kuru and forms of transmissible spongiform encephalopathy. The guy said prions could be infectious agents then other people said no and then somebody was arrested for acting like a Penn State coach and then I forget.
So, I stopped eating brains and left it at that.
I assume you still lurch, at least.
When everything is tuned just right, that happens on about the same timescale as finding the rare tRNA so that translation can proceed.
Dude!
Thanks for writing all that, GB. It's fascinating. And awesome.
This is so awesome! Thanks Gabardine. Biology is so cool.
I've met DB several times. Super cool guy. Incredibly productive. Will collaborate with practically anyone. Incredibly nice for a possible Nobel candidate (someday).
I should add to GB's incredibly great description that the FoldIt problem is orders of magnitude more simple than all the problems that GB was describing. Even limiting ourselves to determining finding only the most stable state, the calculations are so complicated, and there are so many possible shapes, that it would take an eternity to calculate exactly. With all computational chemistry it's a constant compromise. What DB has done, that has rightly made him famous, is to develop really clever algorithms for narrowing down the possibilities and for simplifying the energy calculations so they don't take a year and a half but still give accurate results.
FoldIt is also interesting, since it takes advantage of his optimized energy calculations, but lets gamers do the job of choosing which of the ungodly number of possible shapes to check. And it turns out that gamers have a surprisingly good intuition for finding the lowest energy state, finding the correct answer in a very short period of time.
You're welcome! Woo hook 'em biology.
My mind is blown. Essear, if your current field gets boring, go study this stuff.
Science never ceases to amaze me... Strategy 2 really is remarkable.
Just to say that GB is tha bomb. Thanks. Good stuff.
Cast your mind back to high-school bio and remember that tRNA acts as the adaptor between messenger RNA and protein: each tRNA carries both an anticodon (the complement to a particular codon) and the amino acid that codon calls for.
As I recall, that never would have been covered.* In high school biology we did extremely low level stuff like the name of the pistil and stamen in flowers, memorizing the various kingdoms and some of the phyla, some basic human anatomy, some basic evolutionary concepts, Mendel's bean plants and genetics, maybe a little bit of discussion of DNA at the end, and that was it. I'd bet that's one of the high school classes that has changed the most in the past 20 years.
*n.b. -- I may have been asleep.
Yes, and I echo the thanks for GB's comments. Have you considered a career in the lucrative field of science writing for middlebrows?
I was in high school twenty years ago and we did tRNA.
I think high school biology is typically way more molecular than it used to be. My impression is that this has something to do with the important breakthroughs in understanding molecular biology, and also because it's an easy way to avoid controversy with creationists while still having a fully scientific curriculum.
Yeah, my high school bio teacher, oddly, didn't believe in evolution. So he taught cell and molecular biology and was awesome at it, even all the genetics stuff that clearly had something to do with evolution, but as long as he steered clear from anything organismal he somehow didn't feel any tension with his religious beliefs. It worked, even though it seems suspect somehow.
I should add that (shocking to the Unfoggedtariat, I know), I didn't take "AP" Bio. My memory is based on the bog standard intro high school biology class at a fancypants high school, circa late 1980s.
...even all the genetics stuff that clearly had something to do with evolution
I don't think most creationists have trouble with natural selection so long as you don't say it could create a new species. But, I wouldn't know for sure because I mostly paid attention to how to take apart a fetal pig without vomiting from the smell of formaldehyde.
178 was me. I didn't take AP anything as my school was too small to offer it.
Oh, I forgot about the fetal pig. Totally fucking gross and also seemed, quite annoyingly, to reward kids with better manual dexterity.
*Apologies for turning the thread in a dumb direction -- if smart people who actually know things want to keep writing, please do so!
We made a substitute teacher leave the room because of the fetal pig.
I just checked online, and Fancypants Academy now has a specific course on "Molecular Genetics" that appears to feature extensive lab work in "DNA manipulation" (is this plausibly feasible for a high school?).
The Bio for dumb kids class that I took appears to give 1/2 a semester to the study of "genetics (classical and molecular) and nucleic acids." So I guess things have changed.
...lab work in "DNA manipulation" (is this plausibly feasible for a high school?
Anybody can irradiate their balls.
183
is this plausibly feasible for a high school?
I did it in HS over 20 years ago.
Check out what undergrads do now with DNA manipulation.
The range of biology courses in American HSs, from central Mississippi to AP in elite Eastern suburbs, is amazingly great.
Apparently, the rural midwest does well, comparatively.
I should add:
I did it in a public HS over 20 years ago. But John, as usual, hits the nail on the head.
Just want to chime in and thank GB for the great summary, and F for clarifying the role of Foldit in all this.
173.last: every time experiments are going poorly.
Actually, I've been toying with the idea of starting a realname science blog to post this kind of thing. I'm not sure I'd be able to keep a solo blog well-fed, though. Other science peeps: if you'd be interested in contributing to an as yet nonexistent blog, drop me an email.
You all should seriously do it.
192 to 191, but also to every comment ever.
I suspect that the Discover blog family would be glad to have you. Maybe not, if they regard it as too technical.
HS bio has definitely gotten more molecular. Annoyingly, that sometimes means that teachers think they can't do any labs at all if they haven't got PCR machines and gel rigs and so forth. Pond water, people: still incredibly cool. Put it under a microscope. Draw it through filter paper: enough clear surface water through the filter and I guarantee the filter will turn green or orange from all the photosynthesizers collected. Keep one bottle in the sun and watch it bloom; put another in the dark and watch it crash. Track the pH of the solution in the bloom bottle and the crash bottle. Mix the water from the bottles and I bet the viruses that escaped their dying hosts in the dark will make the bloom bottle crash. Etc.
In my dream world, there would be an integrated science curriculum in which the kids first study optics, then build their own microscopes, then use 'em on pond water. Kids study chemistry and buffers, then make their pH indicator dyes from cabbage and use them to track solution chemistry above. If you insist, you can run PCR, but only by moving the reaction tubes between water baths at different temperatures.
I suspect that the Discover blog family would be glad to have you. Maybe not, if they regard it as too technical.
There are a bunch of science blog networks these days, and this level of technical explanation is definitely within the range they already have.
You rock at explaining things and sublimation.
197 to 195, not that teo doesn't rock at archeological demystification.
So, translational pausing seems like it would be somewhat easy to integrate into computational models of folding if you knew the relative frequencies of the various tRNA, right? Do people do that?
Alternate possibility: The scientists could rotate in a "Sunday Science" feature on this here website. That pretty much guarantees an audience of morons,* however.
(Possibly, of moron)
Codon frequencies vary from species to species; it's not yet all that well understood but seems to have been a very active avenue for evolution. tRNA frequences tend to vary in concert with codon frequencies, but tRNAs, like any gene product, are subject to differential regulation as the cell requires; so pausing can be a bigger or smaller deal at different times. Then there's the spacing between the codon that triggers the pause and the parts of the nascent protein that are available for folding: you'd want the triggering codon to be, I don't know, 30 or so codons later (though the window size might well vary with the likely alpha-helicity of the intervening sequence) than the last-translated part you want available for folding, to allow for the occlusion of a goodish stretch of protein in the exit tunnel, plus steric constraint immediately around the tunnel's mouth. Also rare codons aren't just deployed to help with folding (or rather, I think this is the current consensus but who knows). All in all, I would guess not trivial to do? Though you could certainly set a flag whenever a really quite unusual codon arises at an appropriate position in the sequence, as long as you don't mind some false positives.
I should note also that I have no idea how common translational pausing is in eukaryotic systems. Bacteria and archaea tend to have smaller proteins; eukaryotes may be more likely to default to using chaperones.
My guess is that the scientists would be hesistant to speak about their precise area, because of the possible lack of anonymity, and might have trouble thinking of slightly tangential areas that they could wax on about very well.
But what would be perfect is if the Unfoggedtariat said "I'm curious about [X]!" and then various lurkers and regulars were pulled out of the woodwork to tell us interesting things.
By which I mean, if you're curious about a topic, email me and I'll post an invitation for our science-minded people to tell us about it.
(My best email is under my name in this comment.)
I've attached my syllabus and I'm curious about everything in Week 14 and 15. Thanks.
I kind of like the way conversations almost spontaneously, if sporadically, emerge. The lesson of the reading group weighs heavily.
[Still don't have time to read GB's explanations, but I will!]
206 -- Done! You might want to wait for a smart person to ask something before posting, though.
This seems like a fine point to say that if anyone else will be at AGU this week, perhaps we could have a highly specific meetup.
On the OT -- church-bazaar items are infamously useless and ugly, even when made entirely within the class and region they're being sold into. Hyp 1, making useful stuff is hard, relaxing market discipline (?) means you won't find much. Hyp 2, bazaar purchasers actively want stuff that demonstrates their virtue in this cause, e.g. by being useless for any other.
But I have gotten superbly made and elegant things at Ten Thousand Villages, so.
Shoot, clew, I knew I ought to go, but didn't have anything ready enough at the abstract deadline. Have fun!
I kind of like the way conversations almost spontaneously, if sporadically, emerge. The lesson of the reading group weighs heavily.
I think heebie's idea to post questions as people as them is a good way to avoid some of the pitfalls. It would be a lot like the Ask the Mineshaft concept, but focused on curiosity rather than advice.
It just needs a name that has sexual innuendo.
Next year. Heck, next year I'll have *data*, God willing and the creek rise appropriately.
Next year, definitely. Fingers crossed for your data.
That was great, GB, thanks!
193: Except "Should I get a PhD in the most obscure thing ever?".
Except "Should I get a PhD in the most obscure thing ever?".
No, but, see, if you do that, it puts you in a great position to answer our idle questions about said obscure thing. It's win-lose!
I know of a field last year where something like 15 faculty positions were listed in North America and rumor has it there were not enough qualified candidates in the running. There may have been enough phds, but not many of them want to teach, at least not right away.
218: That field was "professor of ninja librarianism." Only the failures want to teach.
More stable things have lower free energy, so (with some interesting exceptions) the native state is typically the global minimum, the lowest point on this landscape. For some proteins, it's that easy; the landscape is basically smooth, with few or no other local minima to trap a protein en route to the global min. For others, the landscape is rugged, and it's very unlikely that a nascent protein will find its native state unassisted.
You'd be surprised how similar modern cellular radioplanning models are to this.
duuuuuude. GB, you're blowing my mind up in here. guest post!!!
also, there's still plenty of philosophers lurking around, it's just that many of them don't currently profess philosophy. some had to turn, sadly, to the LSATs.
Awesome posts GB.
Interestingly, you might have heard some of those news stories touting the health benefits of red wine. It seems that a compound(s) contained in red wine up regulates cellular chaperones and therefore decreases the load of misfolded proteins the cell has to deal with.
I really enjoyed those posts, GB! Thank you.
Opened this comment box, and it jumped to the end, as it does, and I saw all these references to GB, and thought, wow, Gaijin Biker is back.
Just to join in the bandwagon, I love this kind of stuff, and would read as much of it as Gabardine wanted to write, wherever it was posted. I grew up reading anthologies of Isaac Asimov's science essays, and have been vaguely looking for someone who does exactly the same thing ever since.
GB, adding to the chorus of appreciation. Have you written a book on biochem at the same kind of level as Chad Orzel's "How to Teach Physics to your Dog"? If not, please do so at once - you have a guaranteed couple of hundred sales right here, I'd think. But can you include a glossary - there are a bunch of terms which I don't think are conceptually difficult, just unfamiliar the way they're used.
GB, while we're at it: Why do you think that the great founding organic chemists are so obscure? I went through the Wiki articles, and as far as I can tell the most famous early organic chemist is Alexander Borodin, composer of "On the Steppes of Central Asia", who as a chemist discovered the Aldol reaction and the Borodin reaction.
Well 221-227 were lovely to wake up to. Goodness me.
AcademicLurker, is this resveratrol, or something else?
chris y, I would be very curious to know which terms were unfamiliar to you. That's one of the hardest things to gauge in doing this kind of writing and a calibration would be quite useful.
John, I...uh. I have no idea, and in fact did not know that Borodin was also a chemist (but who doesn't love the aldol reaction?). I wonder, though—could it just be a different in textbook-writing norms? I want to say that my biology texts did a lot more inserting of BOX 1.1 GREAT PERSON OF SCIENCE type things. Or maybe it's a generational thing? My oldest bio professors were there for great foundational moments in modern biology, and they talk the people, because of course students eat it up; modern chemistry is just enough older that that institutional memory will have faded. Paren, you did history of science for a while, didn't you? Do you know?
"talk the people" s/b "talk about the people", obvs.
I would also say that chemistry, especially organic chemistry if you ignore biochemistry, is one of the hardest fields of science to popularize. Without the connection to biology, it's hard to get people to care.
228: You know, I have no idea....because, uh, in my two graduate level courses, I'm not sure we had a single reading focusing specifically on chemistry. (I focused more on the History of Medicine in the History of Science and Medicine in my own work.) I'd agree that my college textbooks also focused far less on "Great Chemists" than my biology ones.
I'd argue that Justus von Liebig was probably more famous in Europe. And Pasteur did some work in organic chemistry, but was wrong about a fair number of things.
My own theory is that the foundations of organic chemistry didn't involve conflict and dramatic stands, like Galileo and Darwin and Copernicus. Not very anecdotal. Intellectually and otherwise, chemistry seems as exciting and important as the other sciences, but somehow it lacks glamor and news interest. it's always puzzled me.
I got the impression that it was a trifle awkward because all the Great Men of Organic Chemistry were Germans at a time when Germany was our enemy.
Might it be that it's less dramatic-theory driven than other sciences? Great organic chemists added incremental stuff to a structure, rather than upending everything that happened before in one theoretical stroke? I don't actually know enough about OChem to defend this, but it seems possible.
Biology is popular because people care about how they work. Physics can be popularized because people care about where they came from (cosmology), and the very fundamentals of how the world works (particle physics). Chemistry is right in between, and it's hard to tell a good story about why the aldol reaction or the Kolbe electrolysis is important to the man on the street.
I loved my organic chemistry class so much. All those little puzzles. I just hated the lab.
As a basically science-ignorant person, I certainly heard a lot about Linus Pauling. I guess he wasn't primarily or exclusively in organic chemistry. Certainly the Curies, who were chemists, are famous. But in terms of famous scientists it's pretty much theoretical physicists and then everyone else trailing miles and miles and miles behind.
237: I am the opposite of Heebie. The only part of o. chem that was tolerable was lab. In retrospect, I wish I hadn't let my inability to model in my head keep me from doing biochem, as I think I would have really liked it.
The problem is illustrated by the fact that a science that gives you explosions! and drugs! can be considered boring by teenage boys.
Drug-using nerds tend to be very fond of organic chemistry.
I suspect 236 gets it exactly right. The chronology suggested by 234 is a little off; a lot of foundational organic chemistry work (done by Wöhler and Fischer and Kekulé and that lot) was indeed German but was done in the 1800s.
It also seems to me that the chemistry easily made exciting for non-scientists often gets co-opted by the biologists; something like figuring out the structure of DNA requires lots of chemistry, but Watson Crick, Franklin et al are not chemists.
I'm with heebie in 237. My dislike for the lab was partly due to my own ineptitude but definitely not helped by being in the section taught by the sleazetastic V/nce, the TA of Lurve.
Is there an unspoken rule that all O. Chem TAs must be eccentric? Mine made us spell his name correctly on every single thing we turned in - lab reports, quizzes, etc. Like, we got points for that. Or no, you didn't get points for it, you just got points deducted if you didn't do it correctly.
(Granted, there was a long, immigration related back-story that totally explains why it was an issue for him, but still. It was strange.)
The synthesis of urea supposedly refuted vitalism, but for whatever reason there wasn't much long-term furor, though I still occasionally hear health food nuts denying that the chemicals in our bodies are the same as chemicals in a laboratory.
Chemistry also seems unimportant in philosophy of science.
Mine made us spell his name correctly on every single thing we turned in
Perhaps not the highest bar of excellence to achieve?
Lavoisier is famous.
248: It was a very hard name for English speakers to spell, but easily enough memorized. The class was otherwise very hard, and he was a rigorous grader. I think it was his way of upholding family honor* and giving us a mild form of extra credit, but it was all very weird.
*I should note that his emphasis on the correct spelling came from a great disservice done to his family - when his father immigrated to the US in the 70s from SE Asia (and I assume fleeing from a situation that the US created), the immigration officer shortened it because it was too long for the forms, without even notifying his father, leading to many complications.
I have a (very minor) client who's opening a Thai restaurant. Over the phone she gave me a very short name, last name Wong, and I thought that it was going to be a Chinese restaurant calling itself Thai to gain a little cache. Then I got the retainer check, with spectacularly long first and last names, the first syllables of which she uses as her name for stupid Americans. The first name I can kind of get my head around, but the the last is the Thai equivalent to Apu's. "Wong" it is.
Cachet, unless they're trying to gain a small hiding place. </little bitch>.
252: Yes, that's how his name was.
At all costs, my full name, Poonsukporntip Wongtungrantkulsiriporn must not be truncated. Your giggling is music in the ears of my ancestors.
a) More praise for GB. I'm sending this thread to my biologist bff so she'll read the blog more.
b) The incidence of "porn" in Thai names seems like it should have become an in-joke here long ago.
