E-Letter responses to:

perspective: Stanley Fields and Mark Johnston CELL BIOLOGY: Whither Model Organism Research? Science 2005; 307: 1885-1886 [Summary] [Full text] [PDF]

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Response to Beck et al. and Jacobson

Stanley Fields, Mark Johnston   (24 June 2005)

The unicellular, biflagellated, green alga Chlamydomonas reinhardtii

Christoph F. Beck, Heriberto Cerutti, Douglas G. Cole, Ursula Goodenough, Arthur Grossman, Elizabeth H. Harris, Peter Hegemann, Stephen M. King, Pete Lefebvre, Sabeeha Merchant, David R. Mitchell, Krishna K. Niyogi, Gregory J. Pazour, Lynne Quarmby, Jean-David Rochaix, Joel   (24 June 2005)

Observations on Model Organism Research

Lewis Jacobson   (24 June 2005)

Response to Beck et al. and Jacobson 24 June 2005
Stanley Fields Howard Hughes Medical Institute, University of Washington, Mark Johnston Respond to this E-Letter: Re: Response to Beck et al. and Jacobson	In describing a Security Council of E. coli, S. cerevisiae, C. elegans, D. melanogaster and M. musculus, we meant no slight to C. reinhardtii, which certainly has provided insights into biological processes. Nor did we mean to belittle the several other workhorses of experimental biology that we also did not mention in our Perspective. In the political arena, the existence of the UN Security Council does not negate the contributions of citizens from Brazil, India, Italy, or Australia; in the academic world, the presence of the Ivy League does not preclude excellence from a Washington University or a University of Washington; in the automotive industry, the naming of a Big Three does not necessarily mean that Honda and Hyundai make inferior vehicles. Humans need to lump items together – be they creatures, countries, colleges or cars – to be able to discern the patterns that exist in the universe. We ask Beck et al. to grant us the latitude to cluster those few organisms that indisputably have attracted the most attention without reproaching us for ignoring others that have attracted less. Jacobson first makes the familiar assertion that declarations of the end of biology are premature, and we agree, as we explicitly stated in our Perspective. Second, although we believe that yeast will be “solved” in 20 to 30 years (and worms and flies perhaps a decade or two later), this solution will result only in a first-level description of all basic molecular processes. Deeper understanding will require the additional knowledge of protein and cellular function desired by Jacobson, and much more. But even if our forecast proves overly optimistic, some future generation of biologists will eventually have to confront their success and redirect their vision toward more complex questions. Finally, with regard to our alleged anthropocentrism, we thought we were singing a paean to model organism research, but perhaps we were a bit out-of-tune or perhaps some could not hear our pitch. Stanley Fields Howard Hughes Medical Institute, Departments of Genome Sciences and Medicine, University of Washington, Box 357730, Seattle, WA 98195, USA. Mark Johnston Department of Genetics, Washington University Medical School, Box 8232, 4566 Scott Avenue, St. Louis, MO 63110, USA.
The unicellular, biflagellated, green alga Chlamydomonas reinhardtii 24 June 2005
Christoph F. Beck Institute of Biology III, University of Freiburg, Heriberto Cerutti, Douglas G. Cole, Ursula Goodenough, Arthur Grossman, Elizabeth H. Harris, Peter Hegemann, Stephen M. King, Pete Lefebvre, Sabeeha Merchant, David R. Mitchell, Krishna K. Niyogi, Gregory J. Pazour, Lynne Quarmby, Jean-David Rochaix, Joel Respond to this E-Letter: Re: The unicellular, biflagellated, green alga Chlamydomonas reinhardtii	In their recent Perspective “Whither model organism research” (25 Mar., p. 1885), S. Fields and M. Johnston discussed the roles of model organisms in biology, pointing out that yeast and E. coli and other members of a “Security Council” of model organisms were workhorses that were used to discover and dissect many fundamental and conserved processes in biology. We are writing to call attention to the biflagellated green alga Chlamydomonas reinhardtii, another model organism that we feel is very powerful, which was not included in the Perspectives article. The Chlamydomonas research community (website: http://www.chlamy.org/; genome sequence: http://genome.jgi-psf.org/chlre2/chlre2.home.html) has made major advances in several areas of biology, including flagellar structure/function and assembly, genetics of basal bodies/centrioles, chloroplast biogenesis, nutrient responses, light perception, fertilization, and cell cycle control (14). Moreover, Chlamydomonas has served as an outstanding model for photosynthesis and how photosynthetic organisms handle light energy. If we focus on even just one of the areas listed above, the flagellum, Chlamydomonas fulfills several criteria that are likely to predict the continued importance of a model organism. For example, because of the original discovery in Chlamydomonas of the remarkable mechanism that assembles cilia and flagella, we now know that genes whose lesions cause polycystic kidney disease function in sensory transduction in the primary cilium of kidney tubule cells. Informed by the same discovery, the vertebrate hedgehog community is recognizing that cilia are essential in sonic hedgehog signaling in the embryo. Moreover, and fulfilling a second criterion, continued studies of polycystin genes in Chlamydomonas promise to provide deeper insights into the functions of these genes whose lesions are responsible for the most common, lethal, monogenic disorder in humans. Also, because of the great number of flagellar mutants and the ease of isolating flagella in large quantities, unraveling the network of interactions required to transcribe, transport, and assemble the ~600 proteins that compose a flagellum/cilium likely will come primarily from studies in Chlamydomonas. Finally, Chlamydomonas is uniquely well suited to teach us about the widely prevalent and devastating human diseases caused by eukaryotic parasites, since many of these organisms are also unicellular and flagellated. In the future, model organisms, including Chlamydomonas, will continue to be important and will be chosen because of their attributes that allow us to address specific questions and biological processes. Christoph F. Beck Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany. christoph.beck@biologie.uni-freiburg.de Heriberto Cerutti School of Biological Sciences/Plant Science Initiative, E211 Beadle Center - P.O. Box 880666, University of Nebraska-Lincoln, Lincoln, NE 68588-0666, USA. hcerutti@unlnotes.unl.edu Douglas G. Cole Microbiology, Molecular Biology and Biochemistry, Life Science South 142, University of Idaho, Moscow, ID 83844-3052, USA. dcole@uidaho.edu Ursula Goodenough Department of Biology, Washington University, St. Louis, MO 63130, USA. ursula@biology2.wustl.edu Arthur Grossman Department of Plant Biology, Carnegie Institution, 260 Panama Street, Stanford, CA 94305, USA. arthurg@stanford.edu Elizabeth H. Harris Department of Biology, Duke University, Durham, NC 27708-0338, USA. chlamy@duke.edu Peter Hegemann Experimentel Biophysics, Humboldt-University zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany. peter.hegemann@biologie.uni-regensburg.de Dr. Stephen M. King Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3305, USA. sking@nso2.uchc.edu Pete Lefebvre Department of Plant Biology, University of Minnesota, St. Paul MN 55108, USA. pete@biosci.cbs.umn.edu Sabeeha Merchant Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA. merchant@chem.ucla.edu David R. Mitchell Cell and Developmental Biology, SUNY Upstate Medical University, 750 E. Adams St., Syracuse, NY 13210-1605, USA. MitchelD@upstate.edu Krishna K. Niyogi Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA. niyogi@nature.berkeley.edu Gregory J. Pazour Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA. gregory.pazour@umassmed.edu Lynne Quarmby Department Molecular Biology & Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C. Canada V5A 1S6. lynne.quarmby@gmail.com Jean-David Rochaix Department of Molecular Biology, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland. Jean-David.Rochaix@molbio.unige.ch Joel L. Rosenbaum Department of Molecular, Cellular & Developmental Biology, 310 Kline Biology Tower, Yale University New Haven, CT 06520-8103, USA. joel.rosenbaum@yale.edu Win Sale Department of Cell Biology, Emory University, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322, USA. win@cellbio.emory.edu Carolyn Silflow Department of Plant Biology, University of Minnesota, 1445 Gortner Avenue, St. Paul, MN 55108, USA. carolyn@biosci.cbs.umn.edu William J. Snell Department of Cell Biology, University of Texas, Southwestern Medical School, 5323 Harry Hines Blvd., Dallas, TX 75390-9039, USA. william.snell@utsouthwestern.edu David Stern Boyce Thompson Institute & Department of Plant Biology, Cornell University, Tower Road, Ithaca, NY 14853, USA. ds28@cornell.edu George B. Witman University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA. George.Witman@umassmed.edu References 1. B. L. Gutman, K. K. Niyogi, Plant Physiol. 135, 607 (2004). 2. E. H. Harris, Annu. Rev. Plant Physiol. Plant Mol. Biol. 52, 363 (2001). 3. J. D. Rochaix, FEBS Lett. 529, 34 (2002). 4. K. A. Johnson, J. L. Rosenbaum, Trends Cell Biol. 3, 156 (1993).
Observations on Model Organism Research 24 June 2005
Lewis Jacobson University of Pittsburgh Department of Biological Sciences Respond to this E-Letter: Re: Observations on Model Organism Research	Observations on Model Organism Research The Perspective by S. Fields and M. Johnston defending the future of model organism research (“Whither model organism research,” 25 Mar., p. 1885) prompts these observations: 1. Biological triumphalism is almost certainly premature. One recalls with wonder the infamous 1969 pronouncement (by a major participant) that molecular biology was effectively over. 2. Many biologists today implicitly assume that identifying “the” function of a gene product ends the story, and this may be true in some instances. Yet it is increasingly evident that a gene product may have diverse functions in different cells or tissues, at different points in the life of those cells or tissues, or under various physiological circumstances. Prospecting for such molecular versatility almost demands the simpler context of model organisms and is not often aided by gene knockout techniques such as RNAi, the insights from which often stop at the first developmental chokepoint. 3. We who work with model organisms have always had to endure the reviews of our grant proposals and manuscripts by those who see research on anything less than humans as an irrelevant waste of time and money. One would think that this myopia might have been attenuated by the experience of the past 50 years of biological research, but it is still a problem. Lewis Jacobson Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.