Finding mystery in God’s tinkertoy

Finding mystery in God’s tinkertoy

Image by Mehmet Pinarci (CC BY 2.0)

Originally published 25 April 1994

Forty-one years ago today [in 1953], James Wat­son and Fran­cis Crick pub­lished a paper in the jour­nal Nature announc­ing their dis­cov­ery of the struc­ture of DNA.

What they pro­posed had a com­pelling sim­plic­i­ty: A mol­e­cule in the form of a spi­ral stair­case. The side rails of the stair­case are linked sug­ars and phos­phates. The treads are mol­e­cules called organ­ic bases, arranged as pairs. The bases, four in kind, are ade­nine, thymine, gua­nine, and cyto­sine, usu­al­ly labeled sim­ply A, T, G, and C. Base A always pairs with T; G always pairs with C. The sequence of pairs along the stair­case is the genet­ic code.

Wat­son and Crick added an almost par­en­thet­i­cal remark to their announce­ment: “It has not escaped our notice that the spe­cif­ic pair­ing we have pos­tu­lat­ed imme­di­ate­ly sug­gests a pos­si­ble copy­ing mech­a­nism for the genet­ic material.”

This is what they had in mind: When a liv­ing cell repli­cates, the DNA stair­case unzips down the mid­dle of the “treads.” Each unpaired base attracts its com­ple­ment; each half of the stair­case com­pletes itself. One set of genes becomes two, two become four, four become eight. Life copies itself in a whirling dervish chem­i­cal dance.

The idea is so sim­ple as to be breathtaking.

The search for the genet­ic mech­a­nism was one of the great detec­tive sto­ries of sci­ence, and the dou­ble helix of Wat­son and Crick was its culmination.

As the two sci­en­tists strug­gled to dis­cov­er the struc­ture of DNA, they built a mod­el of the pro­posed mol­e­cule, as tall as their lab was high, with card­board cutouts rep­re­sent­ing chem­i­cal units, sup­port­ed by steel rods and test-tube hold­ers. Pho­tographs show a make-do, jer­ry-built thing, but still the beau­ty comes through: the ascend­ing spi­ral, the step-by-step plan for build­ing a liv­ing organism.

Mod­ern ver­sions of the Wat­son and Crick mod­el can be found today in most sci­ence muse­ums. No expe­ri­ence has so impressed upon me the won­der of mate­r­i­al cre­ation as stand­ing before the giant stick-and-ball mod­el of a DNA strand at the Boston Muse­um of Science.

Stun­ning. Ele­gant. God’s Tin­ker­toy set. The secret of life.

Now, forty-one years lat­er, sci­en­tists con­tin­ue to play with God’s Tin­ker­toy, but in a dif­fer­ent way. Today’s mol­e­c­u­lar chemists do their tin­ker­ing on the screens of pow­er­ful computers.

The images are often spec­tac­u­lar. A cross-sec­tion of the DNA dou­ble helix, dis­played in shim­mer­ing col­or on a com­put­er, is no less beau­ti­ful than the rose win­dow of Chartres Cathedral.

Com­put­ers make pos­si­ble a kind of mol­e­c­u­lar play that would nev­er have been pos­si­ble with stick-and-ball mod­els, much less with Wat­son and Crick­’s card­board cutouts and test-tube clamps. Pro­teins are made to reveal their secrets with a few clicks of a mouse. DNA and RNA strands twist and curl — elec­tron­i­cal­ly.
Huge­ly com­plex mol­e­cules work their ani­mat­ing mag­ic — digitally.

In prin­ci­ple, all of this could be done with mechan­i­cal mod­els; but in prac­tice no one would have the time, the space, or the patience to do it. Com­put­ers open up a vast cyber­space for mol­e­c­u­lar mod­el­ing, in which mol­e­cules can be dig­i­tal­ly assem­bled and manip­u­lat­ed at essen­tial­ly the speed of light.

What is par­tic­u­lar­ly fas­ci­nat­ing about these devel­op­ments is that we are allowed to par­tic­i­pate visu­al­ly in the research, even if we don’t under­stand very much of the sci­ence behind it.

Our sit­u­a­tion is rather like that of wor­shipers in the great cathe­drals of the Mid­dle Ages. They may not have grasped much meta­physics or the­ol­o­gy, but they saw the ideas of philoso­phers and the­olo­gians embod­ied in stone and light. In the same way, com­put­er-gen­er­at­ed mol­e­cules make vis­i­ble the hid­den
machin­ery of life.

There are those — per­haps the major­i­ty of Amer­i­cans — who decry this new knowl­edge of life. They are repelled by the idea that life can be reduced to Tin­ker­toy mol­e­cules inter­act­ing chem­i­cal­ly, fol­low­ing rules that can be pro­grammed into a com­put­er. Sci­en­tists, they say, are rob­bing us of the mys­tery of life.

Non­sense! The Goth­ic cathe­drals did not dimin­ish the mys­tery of God, nor do com­put­er images of DNA and pro­teins dimin­ish the mys­tery of life.

Erwin Char­gaff, who con­tributed might­i­ly to our under­stand­ing of DNA, wrote: “It is the sense of mys­tery that, in my opin­ion, dri­ves the true sci­en­tist; the same blind force, blind­ly see­ing, deaf­ly hear­ing, uncon­scious­ly remem­ber­ing, that dri­ves the lar­va into the but­ter­fly. If the sci­en­tist has not expe­ri­enced, at least a few times in his life, this cold shud­der down his spine, this con­fronta­tion with an immense invis­i­ble face whose breath moves him to tears, he is not a scientist.”

Observ­ing com­put­er images of the new mol­e­c­u­lar biol­o­gy, I have often felt a cold shud­der down the spine. It is hard to imag­ine how any­one would not feel it.

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