We Are All Superfluous
Sean Carroll is dissatisfied with Pope Giblets
Some time back I suggested that Pope Benedict, the erstwhile Josef Ratzinger, may not have been the best choice to help Christianity broaden its appeal in secular Western societies. Condemning gay marriage and casting doubt on evolution, for starters, wouldn't seem to be effective strategies. Now it appears he might be going for the trifecta: coming down against Harry Potter (via The American Sector).
As with many seemingly paradoxical situations (The "twin paradox," the "EPR paradox"...), there's a flawed assumption at the root of the problem here. Like many people who are mystified by the Pope's actions, Sean is assuming that the Catholic church is trying to "broaden its appeal in secular Western societies." Or that it would be a good idea for them to do so.
I think the proper conclusion to draw from recent events, starting with the selection of Ratzinger as Pope, is that they don't really feel compelled to try to appeal to secular and liberal Westerners. And, really, it's not hard to understand why they would make that decision, given that something on the high side of 80% of the world's population is not secular Western types.
Also, even in secular Western societies, the religious denominations that are doing really well are the intolerant wing-nutty ones, not the sensible and moderate ones. Put that together with the population thing, and it's sort of hard to see the upside of tolerance for the Church.
Yeah, they could take some steps that would make the Church more appealing to secular Western societies. But they don't need to, and it shouldn't shock anybody when they opt not to.
Let the Backlash Begin
It's no Penguin Baseball, but it's mildly amusing.
Playing Out the String
The topic of the moment among the super-ultra-geeky is probably the Strings 2005 meeting on, you guessed it, string theory. Jacques Distler is providing incomprehensible commentary from the meeting itself (his reports start here, and please note, I'm not saying he's wrong or deliberately misleading, just that I can't make heads or tails of it, as I am not a string theorist), while Peter Woit spits venom from a distance. You can almost certainly find more middle-of-the-road reports on the Web, but these two pretty much cover the opposite poles, as you could deduce from Lubos Motl calling down a pox on both their houses (presumably, said pox would cause their blogs to sprout a dozen useles gewgaws and automatically refresh every ten freaking seconds...).
Despite my fairly frequent tweaking of string theorists here, I'm fairly agnostic about the theory itself. They may very well be on to something-- I really can't judge, because I have no clear idea what the theory is. And, of course, it's a little hard to really align myself with Woit, many of whose posts on the subject call to mind the adjective "spittle-flecked".
The biggest obstacle to my taking string theory more seriously is probably string theorists themselves. Whatever complaints I may have about difficult-to-follow chemistry talks, they pale in comparison to the problems I have with string theorists, who can't seem to manage to explain things in a way that makes sense to people in other parts of their own discipline (i.e., me). And then there are statements like this bit from a Michio Kaku article in Discover (quoted somewhat selectively by Woit here, and available only to subscribers at the magazine's site):
Some theorists, myself among them, believe that the final verdict on string theory will not come from experiments at all. Rather, the answer may come from pure mathematics. The principal reason predictions of string theory are not well defined is that the theory is not finished. The underlying mathematics of string theory was accidentally discovered by two physics postdocs, Gabriele Veneziano of Italy and Mahiko Suzuki of Japan, working independently in 1968. The theory has evolved in fits and starts ever since. Even its greatest proponents agree that the final version has not yet been determined. When it is, we may be able to put it to a mathematical test.
If string theory is sound, it should allow us, mathematically, to compute basic properties of the universe from first principles. For instance, it should explain all the properties of familiar subatomic particles, including their charges, mass, and other quantum properties. The periodic table of elements that students learn in chemistry class should emerge from the theory, with all the properties of the elements precisely correct. If the computed properties do not fit the known features of the universe, string theory will immediately become a theory of nothing. But if the predictions accurately match reality, that would represent the most significant discovery in the history of science.
When proponents of a theory argue with no trace of irony that their theory will never find any proof beyond mathematical elegance, and don't really find anything wrong with this state of affairs, well, it's a little hard to take the whole thing seriously as science.
("What about the interpreation of quantum mechanics, and the measurement problem?" you ask. "Shut up, you!" I reply.)
In the recently-booklogged Killing Yourself to Live, Chuck Klosterman spends the better part of a full page talking about how one guitar squeak in the first five seconds of Fleetwood Mac's "I Don't Want to Know" is the best moment of the entire Rumors album. It's fairly typical of his music writing-- he makes a very detailed and literate argument for why this ought to be true, and yet, it seems sort of ridiculous to claim that five seconds make the whole album, or even the whole song.
And yet... The single of the moment in Chateau Steelypips (for me, at least) is "Your Little Hoodrat Friend" by the Hold Steady (you can download the MP3 at the band's site). It's a very strange little song. The lyrics paint a recognizable picture of a woman with Issues (putting the song solidly in the "She Talks to Angels" subgenre), but they're not likely to be mistaken for Dylanesque poetry. They don't even rhyme, and they're not sung so much as declaimed loudly over the music.
And yet, I've been earwormed with this song for almost two weeks, now. And I put the whole blame on a two-second (if that) guitar break in the middle of the chorus. It's about seven notes, and all the other noises stop except for this chugging guitar riff. It's not flashy or complicated, but you can't help air-guitaring that bit when it comes around (twice in each chorus, for a total of six appearances). It ties the whole song together, and makes it inescapable for me.
So, while Klosterman is probably overstating his case (I'm not familiar with the Fleetwood Mac song in question), it's certainly not out of the realm of possibility that five seconds at the beginning of a song could be the high point of the whole thing. It's hardly the only example, either. There's a little acoustic guitar thing in the Old 97's "Big Brown Eyes" (four or five chords on the back-beat, starting after "port" in the line "She's a port... in a storm," that I've always loved. And you could easily argue that the one-off "Wham, bam, thank you ma'am" bridge is the highlight of Bowie's "Suffragette City." For a really extreme example, you could make a case that Phil Collins built an entire solo career out of that one drum fill in "In the Air Tonight"...
But, for the moment, it's the Hold Steady, and twelve seconds of chugging guitar...
Don't Mess With Chemists
After posting the synthetic chemistry guide yesterday, I checked my email, and found yet another new type of spam:
Sodium Percarbonate Multifunctional Detergent Raw Material
See, this is what I get for talking about chemistry...
Extra Bonus Typo from the message body:
SPC is the best bleahing ingredient for detergent.
That's just great, because I've always wanted my detergent to be a little more... bleah.
Three small-ish items that I'm pasting into one big post, because our DSL connection is doing a wonderful dial-up impression lately.
1) Let the Mountains Take Care of Themselves:
I saw the latest outrageous pseudonymous "First Person" piece in the Chronicle of Higher Education on Friday, but I was on my way out the door, and didn't have time to post about it. Happily, it was more or less dealt with while I was out of town, at (among others) One Man's Opinion, The Little Professor, and by Timothy Burke, twice.
I would quibble slightly with the recommendation that would-be academic bloggers blog pseudonymously in order to avoid offending crotchety types like "Ivan Tribble." The common practice of totally re-shaping your life in an attempt to maximize your chances of getting tenure is one of the more pathological side effects of the tenure system, and I think you need to draw a line somewhere.
I'd go into my feelings about this at greater length, but I'd like to get tenure some day.
2) Get That Man a Think-Tank Job:
Fred Clark at Slacktivist has a new series of posts (one, two, three, four) that demonstrate why he's one of my very favorite liberal bloggers. There's been a lot of renewed discussion about "Intelligent Design" creationism lately, but Clark put a human face on several aspects of the stories. He also confronts the fundamentalists on their own ground, explaining why they're wrong in religious terms, not just by insulting them.
(I'll admit, though, that I'm not wild about the first post in the series-- I wouldn't go as far as PZ Myers does, but teaching false information (even under the flimsy cover of Last Tuesday-ism) is a major problem. The second and third posts in the series are brilliant, though.)
I realize he's entirely too reasonable to make it as a pundit, but in the alternate universe where I have a trillion dollars with which to support progressive political causes, he'd be heading his own institute.
Watch Out For That--
Sometimes, you just need to post a link to a site put together by people with entirely too much free time. Crash Bonsai is that site.
(Via a mailing list.)
Notes Toward a User's Guide to Synthetic Chemistry Talks
Summer days are here again, which means the return of the annual summer student research seminar. There's a local tradition of having all the students doing on-campus research give 15-minute talks to all the other summer students. In principle, I think this is a very good idea, as it gives the students some practice at public speaking, and can help form some sense of community among the sciences.
In practice, I'm less happy about it, because I wind up sitting through a lot of nearly incomprehensible talks, most of them dealing with the synthesis of some molecule or another. Over the past several years, I've slowly begun to develop an understanding of how to interpret these talks, but the students who are new to summer research are completely at sea. This has a tendency to make them sort of cynical about the whole business, and undercut the very sense of community that the talks are supposed to be building.
Anyway, the following is a somewhat flippant summary of my conclusions about synthetic chemistry talks by way of (not entirely serious) guidance for non-chemistry students attending these talks.
Recognizing a Synthetic Chemistry Talk
There's no foolproof way to know for sure what you're in for (though the word "synthesis" in the title is a dead giveaway), but knowing some key classes of words can help you spot talks that are likely to be about chemical synthesis. Various "-tion" words ("methylation," "intercalation," "purification") are pretty good markers, though they occasionally show up in molecular biology talks as well. Active verbs are likewise a hint.
A good rule of thumb might be: If there's more than one word in the title that you're not sure how to pronounce, odds are good it will deal with chemical synthesis.
The Four Stages of Synthetic Chemistry Talks
These talks always follow the same basic form, and can be broken down into four stages:
Stage One: "Here's this thing we're trying to make." This is usually accompanied by a picture consisting of a bunch of hexagons, and maybe a ribbon diagram or some other three-dimensional model. Stage One will occasionally include an explanation of why they're trying to make whatever the thing is, but don't count on it.
Stage Two: "Here's the stuff we start with." This will include a couple of diagrams showing different arrangements of hexagons. The jargon will get pretty thick, here, but almost all the strange words will be names of different parts and sub-parts of molecules. See the "Guide to Jargon" below.
Stage Three: "Here are the steps in the process." This will include at least one slide showing multiple diagrams of hexagons, with arrows between them. The jargon will again be pretty thick, but here, all the strange words will refer to methods of sticking pieces of molecules together. See the "Guide to Jargon" below.
Stage Four: "Here are some graphs to prove we ended up what we wanted." This is the stage with the greatest variety of slides. Data graphs may include (but are not limited to) pictures of chart recorder traces, blobby photographs of electrophoresis gels, or pictures of pencil marks made on chromatography films. You'll also get the occasional bar graph or scatter plot.
If you listen carefully, you can easily identify these four stages.
Guide to Jargon
The key here is, don't sweat the details. The confusing jargon terms all break down into two categories:
Pieces of Molecules: Words like "ligand" and "R-group" and "imidazole" and "aromatic ring" all refer to pieces of molecules. These are things that need to be stuck to other things in order to get to the end final product. These usually occur in Stage 2.
You might find it helpful to construct a mental look-up table mapping chemical terms to bits of apparatus:
"Benzene Ring" ⇒ "Vacuum Chamber"
"R-Group" ⇒ "Ion Pump"
"Ligand" ⇒ "Vacuum Window"
And so forth. Every time you hear a new term, assign it the name of another piece of apparatus.
Assembly Methods: Words like "Grignard reaction" or "ligand exchange" or "catalysis" refer to different methods for getting the various pieces of molecules to stick to one another, and indicate that you're reached Stage 3. Think of these terms as different tools used to connect the bits of apparatus.
You might find it helpful to construct a look-up table as you go along:
"Grignard Reaction" ⇒ "Pipe Wrench"
"Ligand Exchage" ⇒ "Phillips-Head Screwdriver"
"Catalysis" ⇒ "Five-Minute Epoxy"
And so forth. Every time you hear a new term, assign it the name of a new tool.
Using these tables, you can easily translate sentences like "We attach the imidazole to the aromatic ring with a Grignard reaction" into "We bolted the ion gauge onto the vacuum chamber with a pipe wrench." The resulting constructions might not actually make sense in experimental-physics terms, but it will get you the basic idea.
The key thing to remember here is that this information is not at all essential unless you plan to replicate the experiment. Hence the analogy: the fact that you bolted the ion gauge to the vacuum chamber is absolutely critical; the fact that you did it with a pipe wrench is really interesting only to specialists.
Guide to Data Plots
The key to interpreting the data plots is that they always come in pairs (at least). There will be one picture showing the signal from the initial reactants, which will consist of a set of peaks, or little photographic blobs, or pencil marks. Then there will be a second set, showing the signal from the same method applied to the products of the reaction. This will be a different set of peaks, blobs, or pencil marks.
The entire point of this section of the talk is to note that the peaks, blobs, or pencil marks in the second picture are in different places than the peaks, blobs, or pencil marks in the first picture. Success is defined as the disappearance of the peaks, blobs, or pencil marks corresponding to the reactants, and the appearance of the peaks, blobs, or pencil marks corresponding to the products.
Peaks, blobs, or pencil marks that are in the same places in both pictures are invariably due to solvents. The speaker will often pretend that these don't exist. Humor them.
Guide to Questions
There are innumerable questions of the form "Why did you use that reaction, rather than this reaction?" that can be asked, and probably will be asked by somebody. These are functionally equivalent to "Why did you use a pipe wrench for that? Wouldn't a socket wrench be easier?" The answers will be really technical, and you probably won't understand them, but if you keep the tool analogy in mind, you'll at least have a sense of what's going on.
If you absolutely need to ask a question, remember that the crucial figure of merit for these talks is the "yield," which basically means "How much product do you get for a given volume of reactant?" If the speaker hasn't mentioned the yield specifically, you can't go wrong asking "What's the yield like?"
If they have stated the yield, ask "How does the yield stack up against other methods of producing this stuff?"
If they have stated the yield, and compared it to existing methods, and you still feel a need to ask a question, ask about the solvent peaks/ blobs/ pencil marks.
Questions of the form "Why are you trying to make this stuff in the first place?" are usually considered unsporting.
(Of course, similar guides could easily be prepared for various categories of physics talks (as I remarked to some peope at the Gordon Conference, the Generic Quantum Information Question is either "What about scalability?" or "What about the decoherence rates?"). Offended academic chemists should feel free to retaliate with snarky physics guides.)
Are you sure you didn’t fall asleep during a synthetic
chemistry talk and wake up during a biochemistry talk?
“electrophoresis gels” and lots of time spent playing
“find the spot” are more biochemistry things. Anyhow,
you also missed stage 3a: “no one knows the trouble
I’ve seen” or “I ran a lot of reactions that didn’t
work.” If you ask your questions right, you can change
this one to “My advisor is an idiot; he thought this
would work.” And “could you do that enantioselectively”
is always a good question, even if there aren’t any
Brian Ledford, 2005-07-12, 7:47am [link]
Are you sure you didn’t fall asleep during a synthetic chemistry talk and wake up during a biochemistry talk? “electrophoresis gels” and lots of time spent playing “find the spot” are more biochemistry things.
There have been a lot of bewildering biochem talks as well, so it’s possible. A more likely explanation is that I’m misremembering what the blobby photographs were from. There have definitely been blobby photographs in a lot of these talks.
Anyhow, you also missed stage 3a: “no one knows the trouble I’ve seen” or “I ran a lot of reactions that didn’t work.”
There’s also a 3b, namely “These are the reactions we plan to run, but haven’t gotten to yet.”
And “could you do that enantioselectively” is always a good question, even if there aren’t any stereocenters.
Maybe, but that would require working out how to pronounce “enantioselectively”...
My wife, reading over my shoulder, mentions that “What about scalability” is a fine general purpose synthetic chemistry question as well as a quantum information question.
Rich Y., 2005-07-12, 9:36am [link]
From an inorganic chemist, some other comments (with any eye toward making things even more usable).
On the recognition front, the phrase “novel and elegant” is almost certainly a dead giveaway, although granted it nearly always immediately precedes “synthesis”. Similarly, the word “steric” is a fairly good indicator of a chemistry talk more generally.
On stage One: ribbon diagrams are more of a biochemistry thing. Any talk that comes from a professor should include something on the why, and that’s a skill they need to start to teach their students. It’s usually an important part of why the professor is interested in this area in the first place.
On stage 3: think of the arrows as being like the assembly directions on a piece of flat-box furniture, if they’re done well. It’s showing you how different parts of the molecule are coming together to make the thing you want. (If the phrase “reaction mechanism” shows up, the arrows are definitely showing the movement of electrons, rather like a circuit diagram.)
On stage 4: If they’re talking organic synthesis, expect graphs of NMR spectra, and maybe IR. (These are the things that might look like chart recorder traces, but few chemists are actually using chart recorders anymore.)
On assembly methods: it’s probably worth including a spot there for “cross-coupling”, which has become a rather common class of assembly reactions in the last few years.
On guide to data plots: If they haven’t somehow marked the constant peaks on the plot, you’re perfectly within your rights to call them on it. An asterisk above the peak is common. (Solvents produce known peaks for different techniques of measurement….)
A last great general-purpose question is “where does this project go from here?”
and, the only bit of snark: N-auntie-Oh-selectively
Longer than I meant it to be, but maybe still useful.
Jeff Dougan, 2005-07-12, 9:58am [link]
A good thing to remember about hard-to-pronounce names of molecules or parts of molecules is that chemists themselves don’t seem to be able to agree on how to pronounce them, and don’t seem to really care, either. Pronounce it any old way, and at worst they’ll think you learned it from a famous Hungarian, possibly one with a Nobel prize.
The biochem people really like blobby photos and ribbon diagrams. The real key to telling if you are in a biochemistry talk is the inevitable slide with a dozen DNA or protein sequences printed in tiny type with a complex color code indicating which parts of which sequences are similar to each other. This is invariably introduced with the comment, “I know you can’t read this from out there, but this indicates….” I think they all just use the very same slide, since we can’t read it, after all.
Damnit! I put a Grignard Reaction through my ligand. Now catlysis is required!
Oooh. This is fun!
Jeff, 2005-07-12, 11:55am [link]
Jeff Dougan: On stage One: ribbon diagrams are more of a biochemistry thing.
A lot of the chemistry activity locally is biochem-related. Two of the three biggest synthetic projects are working on making molecules that mimic some aspect or another of some biomolecule or another.
Any talk that comes from a professor should include something on the why, and that’s a skill they need to start to teach their students. It’s usually an important part of why the professor is interested in this area in the first place.
To be fair, these are fifteen-minute talks, which doesn’t allow a lot of time for putting things in context. And the big picture is really the hardest thing for students to pick up, so it’s not surprising that they don’t do a very good job explaining the ultimate goals of the work.
Still, from where I sit, the synthetic chemsits are very consistently the worst in terms of motivating the work in question.
On stage 4: If they’re talking organic synthesis, expect graphs of NMR spectra, and maybe IR. (These are the things that might look like chart recorder traces, but few chemists are actually using chart recorders anymore.)
The figures in question are usually NMR spectra. And they seem to go to impressive lengths to make them look exactly like chart recorder traces…
Michael Pereckas: The real key to telling if you are in a biochemistry talk is the inevitable slide with a dozen DNA or protein sequences printed in tiny type with a complex color code indicating which parts of which sequences are similar to each other. This is invariably introduced with the comment, “I know you can’t read this from out there, but this indicates….” I think they all just use the very same slide, since we can’t read it, after all.
Yeah, we get a lot of those, too.
I’ll have to start looking more closely at those, to see if the color patterns change or not. You may be on to something here…
Other Jeff: Damnit! I put a Grignard Reaction through my ligand. Now catlysis is required!
I think you mean “cross-coupling,” which is what maps to “Torr Seal”...
You remind me of the Old Sleepy Emeritus Story.
Time was, back in the day, there was an Old Physiologist, what won a buncha Nobel Prizes or something, and he’d come to all the Biology seminars and fall right asleep in every one—snoring and nodding and snurking through the whole thing. Then, see, he’d always wake up a bit because of the applause, and he’d perk up and rub his eyes while a couple of other people asked their questions, and then he’d ask his question: What is the role of calcium in this phenomenon?
And, see, it’s always a good question, in biology.
Still works: You can use it in practically any molecular biology, biochemistry, pathology, cellular physiology, ecology, medicine, or theoretical protein folding seminar, with little or no amendment or modification.
So now you know all you need about another discipline, too.
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Quick Readercon Notes
We drove down to the Boston area this past weekend, to visit Kate's parents, and go to Readercon. It was a small and very book-ish con, but there were some interesting things said, some of which I may comment on at length later. Three quick things that I'll note now:
1) Samuel R. Delany on the way that literary genres originate in the desire of readers for more of a particular thing:
"Why are there women? Because millions of people-- some of them men, some of them women-- find women incredibly sexy and desirable. That's what keeps women coherent as a genre."
2) Scalzi Egoboo Update: There was a stack of copies of Old Man's War on Larry Smith's table in the Dealer's Room, with a Post-It on the top copy saying:
Starship Troopers done better
3) Kelly Link is very cool, and everybody should buy her new collection, Magic For Beginners, just for the title story (several of the other stores are also excellent).
I'll probably try to see if I can make something coherent out of my objection to one line of comments in the "Things You Know But Can't Prove" panel, but there's no guarantee. The important thing is, it was a good weekend, and now it's back to work.