as smiling soreassuringly. He took his time to explain.At some point, - PDF document

as smiling soreassuringly. He took his time to explain.At some point, David said, the field reaches a stage atwhich models, that seemed so complete, fall apart, pre!dictions that were considered so obvious are found to bewrong, and attempts to develop wonder drugs largely fail.This stage is characterized by a sense of frustration at thecomplexity of the process, and by a sinking feeling thatdespite all that intense digging the promised cure!all maynot materialize. In other words, the field hits the wall,even though the intensity of research remains unabatedfor a while, resulting in thousands of publications, manyof which are contradictory or largely descriptive. Theflood of publications is explained, in part, by the sheeramount of accumulated information (about 10,000papers on apoptosis were published yearly over the lastfew years), which makes reviewers of the manuscripts asconfused and overwhelmed as their authors. This stageBiochemistry (Moscow), Vol. 69, No. 12, 2004, pp. 1403!1406.Copyright © 2002 by CELL PRESS.DISCUSSIONS0006!2979/04/6912!1403 ©2004 MAIK ÒNaukaCan a Biologist Fix a Radio? Ñor, What I Learned while Studying ApoptosisY. LazebnikCold Spring Harbor Laboratory, Cold Spring Harbor,New York 11724, USA; E!mail: lazebnik@cshl.org Y (Moscow) Vol. 69 No. 12 2004can be summarized by the paradox that the more facts welearn the less we understand the process we study.It becomes slowly apparent that even if the anticipated gold deposits exist, finding them is not guaranteed. Atthis stage, the Chinese saying that it is difficult to find ablack cat in a dark room, especially if there is no cat,comes to mind too often. If you want to continue mean!ingful research at this time of widespread desperation,David said, learn how to make good tools and how tokeep your mind clear under adverse circumstances. I amgrateful to David for his advice, which gave me hope and,eventually, helped me to enjoy my research even after myfield did reach the state he predicted.At some point, I began to realize that DavidÕs para!dox has a meaning that is deeper than a survival advice.Indeed, it was puzzling to me why this paradox manifest!ed itself not only in studies of fundamental processes,such as apoptosis or cell cycle, but even in studies of indi!vidual proteins. For example, the mystery of what thetumor suppressor p53 actually does seems only to deepenas the number of publications about this protein risesabove 23,000.The notion that your work will create more confu!sion is not particularly stimulating, which made me lookfor guidance again. Joe Gall at the Carnegie Institution,who started to publish before I was born, and is an authorof an excellent series of essays on history of biology [1],relieved my mental suffering by pointing out that a period e com!ponents one at a time or to use a variation of the method,in which a radio is shot at a close range with metal parti!cles. In the latter case, radios that malfunction (have aÒphenotypeÓ) are selected to identify the componentwhose damage causes the phenotype. Although removingsome components will have only an attenuating effect, alucky postdoc will accidentally find a wire whose defi!ciency will stop the music co Y (Moscow) Vol. 69 No. 12 2004fundamentally different from objects studied by engi!neers. What is so special about cells is not usually speci!fied, but it is implied that real biologists feel the differ!ence. I consider this argument as a sign of what I call theurea syndrome because of the shock that the scientificcommunity had two hundred years ago after learning thaturea can be synthesized by a chemist from inorganicmaterials. It was assumed that organic chemicals couldonly be produced by a vital force present in living organ!isms. Perhaps, when we describe signal transductionpathways properly, we would realize that their similarity tothe radio is not superficial. In fact, engineers already seedeep similarities between the systems they design and liveorganisms [2].Another argument is that we know too little to ana!lyze cells in the way engineers analyze their systems. But,the question is whether we would be able to understandwhat we need to learn if we do not use a formal descrip!tion. The biochemists would measure rates and concen!trations to understand how biochemical processes work.A discrepancy between the measured and calculated val!ues would indicate a missing link and lead to the discov!ery of a new enzyme, and a better understanding of thesubject of investigation. Do we know what to measure tounderstand a signal transduction pathway? Are we evenconvinced that we need to measure something? AsSydney Brenner noted, it seems that biochemistry disap!peared in the same year as communism [3]. I think that aformal description would make the need to measure sys!temÕs parameters obvious and would help to understandwhat these parameters are.An argument that is usually raised privately is why tobother with all these formal languages if one can make aliving by continuing with purely experimental researchthat took years to learn. There are at least two reasons.One is that formal approaches would make our researchmore meaningful, more productive and might indeed leadto miracle drugs. A more immediate reason is that formalapproaches may become a basic part of biology soonerthan we, experimental biologists, expect. This transitionmay be as rapid as that from slides to PowerPoint presen!tations, a change that forced some graphics designers tolearn how to use a computer and put others out of work.Of course, a plea for a formal approach in biology isnot new an esoteric tool that is considered useless by many exper!imental biologists, to a basic and indispensable approachof biology.The question is how to facilitate this change, whichis not exactly welcomed by many experimental biologists,to put it mildly [12]. Learning computer programmingwas greatly facilitated by BASIC, a language that was notvery useful to solve complex problems, but was very effi!cient in making one comfortable with using a computerlanguage and demonstrating its analytical power.Similarly, a simple language that experimental scientistscan use to introduce themselves to formal descriptions ofbiological processes would be very helpful in overcominga fear of long!forgotten mathematical symbols. Severalsuch languages have been suggested [13, 14] but they arenot quantitative, which limits their value. Others aredesigned with modeling in mind but are too new to judgeas to whether they are user!friendly [15]. However, I hopethat it is only a question of time before a user!friendly andflexible formal language will be taught to biology stu!dents, as it is taught to engineers, as a basic requirementfor their future studies. My advice to experimental biolo!gists is to be prepared.REFERENCES1.Gall, J. G. (1996) Views of the Cell. A Pictorial History, TheAmerican Society of Cell Biology, Bethesda.2.Csete, M. E., and Doyle, J. C. (2002) Science,295, 1664!1669.3.Brenner, S. (1995) Curr. Biol.,5, 332.4.Von Bertalanffy, L. (1969) General System Theory, RevisedEdn., George Braziller, New York.5.Bhalla, U. S., and Iyengar, R. (1999) Science,283, 381!387.6.Bhalla, U. S., Ram, P. T eri, P., Ransick, A.,Calestani, C., Yuh, C. H., Minokawa, T., Amore, G.,Hinman, V., Arenas , D. (2001) Nature,412, 863.13.Kohn, K. W ol. 69 No. 12 2004Fig. 3.The tools used by biologists and engineers to describe processes of interest: a)the biologist view of a radio. See Fig. 2 and text fordescription of the indicated co