T/9 further comments on method. WHEEL OF SCIENCE. Post P/273 August 4, 1989 Review wheel of science and patterns of discovery in light of my own history. (How questions arise? What resources to answer?) o bacterial sex B+T-->FJR idea of biochemical genetics Avery - Gene as a chemical. Bacteria as tool. ! Transform Neurospora. Convergence of ideas (a) opportunity of technique<--> 1)answer an outstanding question 2)open a field ! delta on prior work Didn't work - reversions - but validated method Discover new questions Try it! That worked. Exploitation! conjugal mechanism map & linkage re: are there genes in bacteria physiological genetics. genes-->enzymes get a lot of mutants what's wrong with the one gene one enzyme model - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - o Salmonella Theoretical background prior to experiment E coli x ; Kauffmann-White schema Salmonella ~ Enterobacteriaceae medically important mutants had already been developed the idea of heterothallism; therefore different strains gotten from Lilleengen Rigid canon of ab x cd eventually worked FA! L-form side track (Dienes) Question: what was FA. conditions of production produced by phage ? Harriet Taylor - was he the first to suggest it? (Boyd's phages re lysogenicity in Salmonella. What was timing?) It's phage! --> Idea of transduction [] unify gene transfer preferred crossing for genetic analysis over transduction Exploitation. Understand Kaufmann-White Analyze H1-H2 collaborate with Edwards o Accidental trails - BADS noted and guessed meticulous pedigree work (? Demerec's abortive transduction dates? get details from BADS) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ P21 Betagalactosidase Exploitation. Extract and characterize an enzyme using canonical approaches. The unexpected discoveries: found crypticity.What were hypotheses? permeability? ? to substrate ? to ions or internal organization Na+/K+ any documentation on why those who tried? Did I test any other metal requirements? Also discovered. Baseline activity ---hypothesis of internal inducer This project was motivated by needing a better assay to continue with the gene enzyme work on betagalactosidase. I believe the precedent was nitrophenol phosphate as a prototype of that and other hydrolase assays In order to achieve this mobilized K.P.Link, Martin Siedman (where is he now) Saul Roseman Other lac work. This is methodology. The intersection of mutants (+their reversions) inducers substrates Many other projects. Chemistry was limited Small group; no facilities I cadged samples from Pigman and Stodola Read all possible on sugar chemistry (needed mutants and therefore exploited the EMB medium I knew that Salmonella was lac negative and EMB used for that) Tetrazolium gave the surprise that it was pH sensitive I observed sectoring and that suggested indirect effect in mutagenesis (Auerbach) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Exobiology This is preeminently theory! Interest in Mars since <1938. Had more background in astronomy and cosmology than most biologists. 1957 Sputnik and Haldane and had the model of nuclear energy as a technology for war or for peace. Social-scientific nexus. Few other scientists would forecast such prompt technological expansion and think about planets even before US had launched a satellite. Political threat in that vacuum. All led to quarantine policy and positive planning to include science in space Instrumentation --> own lab --> computers theoretical planning for Mars missions microhabitat and theory of Mars - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Dendral Computer as a Tool and How Exploited. (a) Discovery that molecules are graphs there was no developed theory ?? How apply computers in a novel way to science. What are they good for. (versus paradigm of McCarthy, Newell and Simon) Molecular compositions then molecular graphs I'd surely had known of Wiswesser, and of Henze and Blair but just when? Designing algorithms for molecular composition "Immersion" - can I improve on that description? graph theory development? learn published art computer implications Skepticism about AI Footnotes: Can these retrospective models be substantiated? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Biography as an Art Still learning method. Contra Jacob. Collecting data. Discovered that history was a problem starting 1973 - reply to Stent, Wyatt re Avery 1974 CASBS 1975 Tatum Began to realize how unique my own archival resources were apart from my own personal recollection from memory of great happenings _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Biotechnology In some way half hearted involvement. Pete Farley turned me off. I didn't want to be swallowed up by anything like my own company. So I had more prevision than nitty gritty about getting into it . And in all of the above (and more) spread too thin for maximum impact in any one area but that still may be best marginal value as long as I can take the heat. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Replica plating and indirect selection Methodological need for garnering mutants Introspection of clonal models converged on the use of velvet then the thought of indirect selection and then in turn how to do it in tubes. So this oscillated between a need and theory: with a convergence in very rapid succession. ---------------------------------------- Some self-characterizations. Not yet ordered. o science as a way of life - curiosity - almost religious intensity o interest in applications of science o method: unremitting abstraction or generalization. Example, why a brush --> velvet -->tubes (repl. plating) What is the theory that would account for x. What are range of theories that imaginably could? What if anything is excluded? o the systematic scan - see "Signs of Life" o ring all the changes self-ref'lly: e.g.what other styles are possible? cf AHK and F Jacob o go for broke! No inhibitions about silly or off-beat or prophetic extrapolation. Start things even if they are not finished. Ask what questions are important and neglected, then which ones are feasible. o learn everything possible about (a) new field - even if spread too thin o interdisciplinary convergence. Post 1959 more behavioral science. o " exposition as formal proofs" . see style of P80, P49 and P60. o revelation of method: not necessarily consciously planned Ask "what am I doing" after observing it o use of unconscious - let problem simmer. So many brews at once. o settings - extempore delivery - discipline - stimulation of an audience (can't evade here and now); (see notes on teaching, dialectic Other settings airplane trip, Pescadero cabin, limited distractions. 'waking thoughts -- esp. geometric fantasies o contingent circumstances --> what comes to my attention constant foraging but rarely drop anything o introspection on method, as method. Not always transparent to me how others differ o what am I most usefully qualified for: "self" as instrument [sets of values, social, ...] o self-referential effect: applying method to this case o who else has introspected on method? cf Beveridge (?sent to Altman) o in what other ways could one construct this kind of a chart ? cf HAZ, Larry Holmes, who else's approaches might be _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Penicillin Methodological Needs / \ Data Theory \ / Disciplinary Needs .SH L-forms. What are they? Generated by penicillin Social and intellectual setting Facilities Breadth and distribution of interests o Penicillin lyses growing cells and this was used in the penicillin method o Weibull - sucrose stabilizes protoplasts Needed selective method for auxotrophs How do it? Recall Gladys Hobby. Are L-forms protoplasts? Then methodical study though limited chemistry. Check out citations to Dienes. Implications for mode of action of penicillin. o Review what methods invoked much more chemical theory then used in laboratory. No radioisotopes or chromatography. Experimental ingenuity - e.g. micro manipulation but very limited laboratory chemistry Limited managerial zest (sic!) Strong theory, argument, broad knowledge Intuitions about organisms Very strong theoretical background in biology and chemistry Moderate theoretical background in physics and math CP&M more than most biologists and many chemists _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ F, lambda accidental discoveries prompt analogies --> plasmid concepts Lambda gal. cf Morse. the implicit discovery of defective lambda but not properly followed up Around this time the whole field suddenly changed. The outside became far more competitive and crowded. Special collaborations (Luca, a few students) Still very limited facilities. Did not know how to demand them. Was still very young at UW. No role model for lab head past brief experience with FJR and he did not dominate a group. Accumulation of knowledge yields an infinity of questions. Broadening of interests: genetics as a mission --> somatic cells and immunology --> exobiology --> AI --> algeny Footnote: Stanford: Mistake? to organize a department with larger aims rather than focus on my own lab _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Socio Historical Circumstances Generational b. 1925 precocious autodidact 1935-1941 Columbia College Medical School V-12 unique opportunities lst born son of an Orthodox Jewish rabbi who was himself an immigrant from Israel. Remarkable advantages of New York City. Encounter with Francis Ryan. His objective evaluation of talents --> opportunity to work in self confidence. o Technological optimism 1925-1945. Power of science. The Value of omniscience. Hitler and World War II Escaped communist party. Most antisemitism. Era before reverse discrimination o 1948-1960 NIH, expansion of science (e.g. Stanford) o Genesis of chemical biology. HG Wells style reductionism. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Why such a generalist? o 1) science as a religion --> scientific outlook (? author of of that phrase. Was it Whitehead, Wells or Russell) o 2) curiosity --> integration o 3) responsibility/guilt... Jew, survivor --> applications o 4) self confidence. Early success, parental and teacher esteem no early trauma. Stresses only 1950s; 1961 ff. (latter coincides w/ > sociol.-interpersonal concerns o 5) autodidact. Learned that it was almost too easy to go into new fields _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ---------------- _890905 discovered my introspections re method from Churchkey 12/5/56: -- It then occurred to me that this had been a general pattern in my scientific work. Steps: a) Consider a specific, sometimes a minor technical problem. Because it is restricted, it can be analyzed in its essentials, or else intuitively solved. b) What are the essentials, expressed in the most general form? [Example: replica plating is equivalent to multi-tube selection]. and c) What problems of general import can be solved by this technique? Example: selection for specific genotypes, as used in Neurospora reversion studies, is also applicable to selection for rare recombinants. Example: one cycle of enrichment in replica plating can be reiterated for effective indirect selection. Example: pneumococcus transformation & Salmonella transduction are aspects of same phenomenon; lysogenic conversion is correlated at even a further level. Example: hypertonic sucrose might protect against lysis by other agents besides lysozyme. Not all problems and discoveries are technical. In many cases one has, rather, to frame specific hypotheses and find critical experiments to decide between them. Abstraction is of course a necessary precedent to imagination here too. But I am not sure this has been my strongest technique. Moral: Solve specific problems, narrow enough to be grappled with. The stimulus of this accomplishment, the abstraction of the technique, and its broader application will then usually suggest other soluble problems and approaches. I think that this mental cast has something to do with ways of science (as I think Seymour quoted from Luria): (1) to start with a methodology and find phenomena; (2) to start with a phenomenon and find a rule. Not many people do both well: the biophysicists have generally prospered with (2), which is also safer for graduate students; my own actual emphasis has been on (1). If this is a reflection of talent, it might be better if I did not stick too long with the study of the various systems I uncover, which I have perhaps done or thought I had done. ---------------- 090518 [disc. w/ Noordewier] See T/15! devil's advocacy Always think about kinetic contradictions to thermodynamic expectation [cf folding] [] aversion to 'neural-nets' and other black boxes; in favor of constructive logic schemes. But I use natural selection!!