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nature genetics supplement • volume 32 • december 2002 465

Sharper tools and simpler methods

Geoffrey M. Duyk

doi:10.1038/ng1027

In this issue of The Chipping Forecast, we are witnesses to the adolescence of a class of technologies that are

enabling us to monitor globally aspects of gene expression. Chip-based technologies are specific examples of a

more general trend toward the implementation of systematic and comprehensive methods in biological research.

We need to recognize, however, that these technologies, while seductive, can sometimes be corruptive. In other

words, we must guard against committing the mortal sin of genomics by confusing throughput with output,

which too often blurs the distinction between data and knowledge. Instead, we must maintain the necessary

focus to achieve an ever-more operational understanding of all the molecular components and the interactions

that define a cell or an organism.

“Every real advance goes hand in hand with the invention ofsharper tools and simpler methods” (Professor David Hilbert,International Congress of Mathematicians, Paris, 1900).

The increasingly familiar images of biological arrays or chips,and the characteristic representations of data derived from them,have become icons helping to define this as the era of the HumanGenome Project (Fig. 1). We no longer are amazed that theseapproaches work, or look for the chance to test-drive the latestdevelopment. Instead, we are applying our collective wisdomtowards developing more advanced applications and towardunderstanding and overcoming the limitations of currentmethodology. This enhanced level of scientific discipline,reflected in the reviews published herein, will increase the utilityof these methods and will provide the basis for the next genera-tion of tools and protocols.

Collections of review articles often beg the question: where dowe go from here? So far the principal goal of the Human GenomeProject has been to enumerate the objects of biology (such asgenes, genomes and proteomes) and to describe rudimentaryaspects of their behavior. These projects, which are directed atbuilding an infrastructure of resources and tools, reflect a desireto deconstruct biological processes into their molecular compo-nents. The key challenge for the coming century will be to estab-lish complete molecular descriptions of biological processes thatare sufficiently quantitative and dynamic to allow their predictivemodeling or simulation. Parallel development of enhanced datavisualization tools, in addition to the ongoing challenges of datastorage, computation and analysis will be increasingly central tothese endeavors. In the end, we would like to be able to map geneactivity onto physiological processes.

To achieve these goals, we will need to move beyond studyingindividual molecular components as the fundamental units ofresearch. Instead, the focus will shift towards increasingly com-plex macromolecular assemblies that can be defined as bothphysical entities and functional units. Our attention will need tomove towards pathways, networks, molecular machines,organelles and eventually the cell itself as a unit of work. Toachieve a four-dimensional description of biology, the new tech-nologies must be more quantitative and ‘systems focused’ andwill require that we abandon our ‘destructive methods’ for study-

ing cell biology. Such capabilities are well beyond current tech-nology. The future developments that will enable us to under-stand biological processes at this level of resolution are based onour ability to interface with other disciplines and dissolve the dis-tinctions among biotechnology, information technology andhigh technology.

Short-term technology investmentsThe short-term goal of the Human Genome Project is clearly tocomplete the catalog of ‘molecular objects’. Ultimately, this cata-log will include the identities, structures and annotations corre-sponding to genomes, genes and gene products, as well asinformation on natural variations and covalent modifications. Itwill be important to expand this cataloging effort to other cellu-lar constituents such as metabolites.

A key incentive for investing in and implementing genomictechnologies has been our desire to reduce the time and effortthat a scientist spends assembling the reagents, resources andinformation that are necessary to design and carry out an experi-ment. Logically, current developmental efforts should lead to theelimination of the classical tasks associated with molecular biol-ogy research—freeing the hands and the minds of the scientificcommunity so that it can focus on new types of problems.Towards this end, there are several technology- and resource-related initiatives that are worth considering in the short termthat not only will enhance our biological research capability but,with reduction to practice, will also force us to confront moresignificant biological problems and technical challenges.

Large-scale DNA sequencing projects have been and will con-tinue to be the primary driver behind our comprehensive molec-ular catalog. These projects have not only revealed the sequencesof genes and genomes, and of natural and acquired variants, buthave provided a glimpse of our own evolution as a species andthe evolutionary landscape. They have also enabled molecularbiology to have a significant impact on other fields, such asanthropology, archaeology and environmental sciences. But anexpansion in the scope and scale of sequencing and resequencingprograms (including genotyping) will be governed by cost. Theanticipated short-term changes to our current technologies—such as using microfluidics for reagent and sample handling,

Exelixis, Inc., South San Francisco, California 94083, USA. (e-mail: duyk@exelixis.com)

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466 nature genetics supplement • volume 32 • december 2002

more automated process and information handling, andimproved separation and detection methods—are incremental atbest and may only result in a 5–10-fold reduction in cost.Although such changes will be significant, the logarithmicdecrease in cost that is required to step up to the next level islinked to the development of a fundamentally different sequenc-ing technology. Efforts aimed towards this goal need to beencouraged and supported.

Many current genomics research projects are focused onassembling collections of full-length cDNAs and incorporatingthem into ‘universal vector systems’ that can support a variety oftasks. Despite its obvious value, this exercise is limited by a lackof scalability. Cost and tedium will ultimately end the expansionof this program, and it is unlikely that systematic and global pro-jects directed at incorporating all naturally occurring splice orsequence variants, engineered versions of genes, or gene setsderived from diverse organisms will be undertaken. Instead, weneed to develop efficient and cost-effective methods for synthe-sizing complete genes and proteins and should aspire to methodsfor synthesizing complete mammalian-sized genomes and pro-teomes. These developments will need to go hand in glove withautomated methods for modifying natural and engineered cova-lent proteins and with improved methods for purification andproduct validation. The establishment of a computer-aideddesign/computer-aided manufacturing (CAD/CAM) platformfor molecular biology would simplify sample tracking, reagentdistribution and storage, and would enhance our ability tomanipulate the components of genomes and proteomes. Such aplatform would also propagate more ambitious experimentalobjectives for the Human Genome Project.

Similarly, we should consider developing systematic proce-dures to create comprehensive sets of antibody or antibody-likereagents that are directed against all proteins, their various iso-forms, and other essential molecular determinants. Not onlywould these reagents facilitate the quantification and localizationof biomolecules, they could also be used as tools for manipulat-ing biological activity. Accessing or developing these types ofreagent represents a significant time and cost sink for researchers.The general scientific community needs access to both existingtechnologies and a broader-based resource, as well as encourage-ment to develop alternatives or adjuncts to antibodies and theirassociated experimental protocols. Current experimental chal-lenges suggest that a the development of a global approach to‘indirectly’ label proteins would be a significant driver ofprogress. Labeled reagents could be targeted to act either byselectively binding to, blocking or activating proteins, or by mon-itoring protein function as a substrate or sensor/reporter of a

selected activity. The application of small-molecule chemistry,polymer chemistry or nanotechnology may offer fertile areas forthe discovery of alternatives to antibodies.

Fundamental strategies for studying gene function require thedetection, modulation and/or alteration of the activity or expres-sion of a gene or gene product. Certainly, there will be an expan-sion of projects dedicated to developing systematic methods ofgenerating genome-wide collections and global gene knockoutsin model organisms or cell lines. RNA interference and antisensetechnologies are examples of scalable technologies that are avail-able now and merit immediate consideration. We can also antici-pate improvements in gene and protein switch technology thatwill enable the tunable and/or reversible modulation of gene andprotein activity. These switches will be based not only on classicalprocesses of molecular biology but, as indicated above, also onengineered small-molecule agonists and antagonists, and otherclasses of functional probes. The availability of such resourcesand tools will drive a renaissance in the study of molecular phar-macology. We will need to understand the biology of both thegenes and the molecules that are directed against them. Invest-ment will be required to develop scalable procedures for deliver-ing the knockout, affinity or tagged reagents into a cell or ananimal. Ideal delivery systems will be efficient and will considerissues of selectivity, specificity and the accurate incorporation ofreagents into specific cellular compartments.

Beyond current technologiesThe disruption of ‘function’ by any of the methods discussedabove highlights a deficiency in our ability to quantify globallythe dynamics of gene and gene product activity and the spatialand temporal dynamics of synthesis and turnover. Our capabilityto quantify stable and transient interactions among biomoleculesin vivo is even more limited. These technical gaps are the‘Achilles’ heel’ of current biology—especially if we contemplateextracting the type of information that is needed for a four-dimensional description of biological processes. Although toolssuch as mass spectroscopy or chip-based profiling models thatcan globally monitor changes in aspects of molecular activitiesdeserve increased attention, they are only part of the solutionbecause they are limited by cost, access and the status of our sep-aration and purification technology. Protocols based on thesetypes of technology are also examples of ‘destructive testing’. Thephysical disruption of a cell, as a means to gain access to its con-stituent parts, disengages biology from its appropriate context inspace and time. Unless the community aspires to move on fromthis current working model, it is very likely that the ‘new biology’will remain beyond our reach.

In the long term, the cell itself—as opposed to genes or geneproducts—will become our unit of work. Comprehensive cell-based biology will eventually give way to an enhanced disciplineof ‘molecular organismal physiology’. A substantial impedimentto cell biology research is the quality of the available cell lines,and we will require resources that are better characterized biolog-ically and genetically. The current revolution in stem cell biologymay be a logical starting place for developing a robust set of cel-lular reagents that accurately reflects the underlying biology. Theimplementation of such reagents would provide a powerfulresearch platform; the capacity to shuttle reagents based on stemcells between the culture dish and whole animal systems wouldenable us to study complex interactions between different cellsand between a cell and its microenviroment.

Fig. 1 Biological arrays have become icons of the era of the Human GenomeProject.

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nature genetics supplement • volume 32 • december 2002 467

Another challenge will be the translation of cell-based assaysinto single-cell formats, permitting a more ‘quantal’ approach tobiological research. This will require vast improvements in ourability to detect events from single cells and in our ability tomanipulate, separate and sort single cells or small quantities ofcells. Certainly the emergence of microfluidics and microelectro-mechanical systems (MEMS) devices as well as the continuedadvancement in imaging technologies will have an importantrole in realizing these goals. Finally, current systems for assuringaccess to and distribution of cell lines and experimental animalmodels are not optimal, and these market-based inefficiencieswill need to be addressed.

At the interface of science and societyIn addition to issues related to reagents, tools and procedures, we need also to consider the ‘sociological issues’ that surround technology and its development. One of the most importantconsequences of genomics initiatives has been the introductionof high-throughput technologies to the discovery phase ofresearch. Our reliance on mechanical automation, instrumenta-tion and systems for managing laboratory information has had abig impact on the workplace, making issues of operation, orga-nization and diversification of intellectual capital part of thecompetitive mix.

A fact of scientific research is that ongoing access to a broadlydefined and well-integrated technology base affords a competi-tive advantage. In addition, narrowing technology lifecycles andincreasing expectations of productivity suggest that technology isnot only indispensable, it is increasingly disposable. When con-templating investments in technology, therefore, it is necessary toconsider the development or acquisition of technology, and alsoissues surrounding the maintenance, evolution and integrationof a research platform in the face of rapid progress and shorttechnology life cycles. These challenges are even greater if welook outside our own community and consider the issues thatface emerging countries as we develop the necessary strategiesthat enable them to access technology and its output.

The increasing dependence of the biology laboratory on tech-nology has several implications. Research groups will need moreresources, but also more flexibility and freedom with which tooperate with respect to the allocation of financial and intellectualcapital. For larger research centers to maintain critical mass andmomentum, longer term, stable sources of funding must beidentified. It may be that sources of funding will have to beuncoupled from traditional grant cycles to ensure the necessaryflexibility and capacity to respond to change.

In the absence of change, it is likely that we will witness theemergence of quasi-private research institutes that are looselyaffiliated with academic centers. Such institutes will develop theirown endowments and so will have more direct control over theirresources and intellectual property, and increased flexibility todevelop partnerships with the private sector. As a consequence,the universities will have reduced access to technology and willrisk losing their best faculty staff and students. The gap betweenthe ‘haves’ and the ‘have nots’ will only widen. Genome projectshave established ‘large-scale science’ in the biomedical researchcommunity, thus instigating the inevitable debate over the valueor merits of traditional grant-funded laboratories versus themegacenters. This debate only serves to polarize the scientificcommunity and needs to be redirected towards productive ends.We should use this issue as an opportunity to rethink how toassure access to both technology and know-how and, at the sametime, how to align these resources across the spectrum of activi-ties and responsibilities associated with life science research andits educational objectives.

Biomedical research is a capital-intensive endeavor, and itsever-increasing need for money creates many challenges andopportunities for those seeking funding and for those providingfunds. Speculative in nature, decisions regarding funding invest-ments in technology are inherently more complex than invest-ments that result in short-term tangible gains. The potential scaleof the required investment is large enough to face competitionfrom opportunities outside the biomedical research communityand as such must be justified on the basis of the potential impactbeyond the ‘advancement of science’. Ironically, the decisionmakers are often forced to choose between many diverse optionsand competing priorities but are unlikely themselves to be able tojudge a funding opportunity on its technical merits. Thus, psy-chological factors such as perceived credibility, vision, popularopinion, conventional wisdom and general mood have a signifi-cant impact on decision making. In such an environment, educa-tion and public relations strategies are essential. It is in theinterest of our community to become pro-active in enhancingand broadening science education and in disseminating infor-mation at all levels, including primary, secondary and collegeeducation, and the general public. We must also avoid what somehave called ‘scientism’—an elitist attitude that rationalizes hold-ing at arm’s length the opinion of the public and input regardingour work. Assuring scientific literacy and encouraging dialogueis necessary if we are to continue to push the limits of our tech-nology in the hopes of turning the output of the Human GenomeProject into a true biomedical revolution.

Technology development, distribution and access are greatlyaffected by the ‘gate-keeping’ interfaces between the public, acad-emic and private sectors, such as offices of technology and licens-ing, human subject review boards, the Patent and TrademarkOffice and the Federal Drug Administration. These groups havemany attributes in common. They tend to be under-funded,under-powered, under-supported and under-appreciated rela-tive to the groups with which they interface; but the decisionsthat they make often have profound, far-reaching and long-last-ing effects on research and its affiliated activities. The pressureson these groups are intensifying owing to the rapid pace ofchange in biomedical research, the heightened awareness of thepotential economic and social impact of the research, and theglobalization of research activities. These are issues that demandour attention and require a careful review of operations, proce-dures and policies, and a commitment to evolution of the same.In the current environment, we need to assure both ourselvesand the public that the necessary checks and balances are inplace. We need to view these agencies as partners, not adver-saries, and start promoting mutual understanding and avoidingpaternalism. Ultimately, we must find the correct balancebetween progress and process, and must be willing to invest thetime, effort and capital that is necessary to promote the improve-ment of these systems.

In summary, short-term technology investments and devel-opments should represent logical extensions of our currentefforts to compile the catalog of molecular objects and to elim-inate the traditional tasks of molecular and cellular biology. Aswe complete this program and begin to address issues associ-ated with creating a more quantitative biology that willbecome increasingly focused on issues of cellular and whole-animal physiology, we will need to tackle several technicalissues that require exploration of emerging technologies fromfields that traditionally lie outside biomedical research. Thecontinuing development of technology and its implementationwill be costly and will continue to change the fundamentals ofour scientific culture as well as our interactions with thebroader communities.

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468 nature genetics supplement • volume 32 • december 2002

As David Hilbert said in his famous address in Paris outliningchallenges for the mathematics community in the twentieth cen-tury, “As long as a branch of science offers an abundance of prob-lems, so long is it alive; a lack of problems foreshadows extinctionor the cessation of independent development”.

AcknowledgmentsThis commentary was based on an address originally delivered on 13 December 2001 at Airlie House, Virginia. I wish to thank S. Ebrhimi, J. Green, P. Pospisil and I. Reichardt, my colleagues at Exelixis, for commentsand input.

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