Viz: Proof by Suc­ces­sive Contraindication

Begin the proof in front of a large atten­tive audi­ence. Lis­ten to the audi­ence reac­tion as you tran­scribe the proof onto the black– or white­board. When­ever the audi­ence makes con­traindica­tive noises above a pre­de­fined thresh­old, roll back the proof to the point where the noises began, and pro­ceed in a slightly dif­fer­ent direc­tion from there. Repeat as nec­es­sary, until the con­clud­ing point of the proof is reached, or a Socratic Ped­a­gogic Deficit [Cf.] is about to occur. If you detect that an SPD is about to occur, leave the remain­der of the proof to the audi­ence as an exercise.

Socratic Ped­a­gogic Deficit: In a les­son taught by the Socratic Method, the amount by which the pos­i­tive ped­a­gogic value of leav­ing the “real” answers ambigu­ous is exceeded by the con­fu­sion caused by leav­ing them ambiguous.

You would need to know what Magic: The Gath­er­ing is, I suppose.

But still worth a look — before WOTC comes along and kneecaps them.…

In my expe­ri­ence, a large major­ity of smart and well-​​trained peo­ple (who should know bet­ter) don’t have any clear idea of what it’s like inside a cell. I blame this squarely on bio­chem­istry ped­a­gogy, with its unmen­tioned but implicit lin­eariza­tion of chem­i­cal reac­tion kinet­ics and tacit assump­tion that every­thing can be sep­a­rated into func­tion­ing com­po­nents and stud­ied sep­a­rately: we are taught (and have taught, when we were doing that sort of thing) that all mol­e­cules always bump into each other in iso­lated pairs, and have plenty of time and space to asso­ciate and dis­so­ci­ate as they wish in their intra­cel­lu­lar envi­ron­ment. One that’s fun­da­men­tally no dif­fer­ent from a test tube of dilute pure mol­e­cules we study in the lab. That leads to the sup­po­si­tion that we can infer from lab­o­ra­tory mea­sure­ments of such pure test cases, where we actu­ally assign num­bers to prop­er­ties of pure dilute macro­mol­e­cules, what behav­ior that depends on K_D or K_I will be like inside a cell. We assume that because the nat­ural length scales of supramol­e­c­u­lar com­plexes are so much larger than those of chem­i­cal reac­tion and asso­ci­a­tion events, long-​​range struc­ture has lit­tle or no impli­ca­tion for what hap­pens on the scale of the event.

Which is pure bullshit.

Such a premise is tan­ta­mount to imag­in­ing that the con­tents of cells are per­fectly mixed. If this strikes you as a not-​​unreasonable mod­el­ing assump­tion, espe­cially for math­e­mat­i­cal tractabil­ity, I invite you to ran­dom­ize the con­tents of some of your cells and see how they do. A blender will do in a pinch.

I haven’t had the plea­sure of this rant in a few months, but I was about to start writ­ing about it in the con­text of Syn­thetic Biol­ogy and wrong-​​headed notions of design. And I will. But I needed a lit­tle jos­tle to jump-​​start me. So it is with plea­sure that I’m reminded of David Goodsell’s extra­or­di­nary work on this sub­ject, by way of a link from BioCu­ri­ous to “PDB Mol­e­cule of the Month: Cholera Toxin”.

If you want to make a pos­i­tive dif­fer­ence in our lives, by under­min­ing incor­rect myths held by bio­med­ical prac­ti­tion­ers, send a friend to this stun­ning work of sci­ence and art (be sure to click the three-​​panel graphic to see it at mind-​​numbing size). Ask them how much water there is in between those mol­e­cules. Ask them how metab­o­lism works, in light of those net­works. Ask your bio­chem­istry (or gen­eral biol­ogy) grad stu­dent to point out where they would expect to find the Krebs cycle they draw in sim­pli­fied circles-​​and-​​arrows for­mat on the board in the first week of class — right there, on that map. [It may be a trick ques­tion, for that par­tic­u­lar pic­ture] Then, while they’re pon­der­ing, ask them quickly, “OK. This is eas­ier — how does the infor­ma­tion from the genome get from over there, to over here?”

I think that image, along with Dr. Goodsell’s other port­fo­lio on this theme, is prob­a­bly the most impor­tant work of sci­en­tific art for this cen­tury, and should be plas­tered up on the wall of any lab that’s doing any­thing in any set­ting that involves intra­cel­lu­lar mol­e­c­u­lar dynam­ics and cel­lu­lar physiology.

But that’s just me. What do you think?

(And if you do think it’s ques­tion­able to lie, then I sup­pose it’s even bet­ter to just be lazy and stupid.)

A cre­ation­ist defends his lack­adaisi­cal know-​​nothing igno­rance about mat­ters of fact so glibly, it hurts:

You are cor­rect in that there are 30 total ani­mal phyla; I was writ­ing a piece to explain this con­cept to a gen­eral audi­ence, and I included the chor­dates plus insects. You, as a revered Pro­fes­sor of Biol­ogy, may find my pique with my care­less­ness. Fine(after all, I‘m not a biol­o­gist). Nonethe­less, it does not mat­ter to the argu­ment wether there are 2, 8, 15, 30, or 2000 phila (ouch! my knuck­les!); the point is that we there was no real crossovers between crea­tures. I sus­pect you under­stood my point, but quib­ble over it because you think you‘ve got me. If it salves your ego to gloat, go right ahead! The fact is, the great point you think you scored was wide of the argument.

Heh. “The argu­ment.” There was an argu­ment? I fig­ured it was just a bunch of wrong stuff.

Seri­ously. I said some­thing like this before, PZ: These peo­ple only appear to be talk­ing to you. They’re not. They’re sig­nal­ing one another, count­ing coup and rack­ing up points in an enig­matic and fun­da­men­tally irra­tional social rit­ual that means some­thing only in their sub­cul­ture. This fel­low now can go off and say how he bested you, no mat­ter how much a fool he has actu­ally made of him­self, because he isn’t try­ing to make a point to you, or con­vince you of any­thing.

The evi­dence is right there on the page: no sane per­son could mis­take such an exchange for an attempt to con­vince you. He’s talk­ing to some­body else, and he’s declar­ing some­thing to them: his mem­ber­ship in their tribe, his faith and mar­tyred pride, his supe­ri­or­ity to worldly intel­lec­tu­als and nig­gling arti­fi­cial­i­ties we think of as “facts”, his strength in the face of the Bad Thing you represent.

You, the nom­i­nal cor­re­spon­dent, are irrelevant.

There has to be a good use for this.

[click for orig­i­nal image]

Pub­lished in 1913, this thrilling tale of adven­tures includes “Boy Scouts in a Coal Mine” and “Boy Scouts in Alaska”, plus the mys­te­ri­ously engag­ing short story “Black Art in Cincin­nati”. But do you really care? I do… but do you?

So: Go, thou sopho­moric PoMo remixer, and make some­thing of the pic­ture. I see t-​​shirts. I see posters. I see an entire Band Name, plus the cover of their first album.

[the actual book has already been scanned, and is being munged into the appro­pri­ate for­mat for Dis­trib­uted Proof­read­ers. Watch over at Odd Ends for more info, espe­cially our project data­base.]