Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
ANNUAL REVIEWS
Quick links to online content
Further
ANNUAL REVIEWS INC. is a nonprofit scientific publisher established to promote the advancement of the sciences. Beginning in 1932 with the Annual Review
of Biochemistry, the Company has pursued as its principal function the publication of high quality, reasonably priced Annual Review volumes. The volumes are organized by Editors and Editorial Committees who invite qualified authors to contribute critical articles reviewing significant developments within each major discipline. The Editor-in-Chief invites those interested in serving as future Editorial Committee members to communicate directly with him. Annual Reviews Inc. is administered by a Board of Directors, whose members serve without compensation.
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
1990 Board of Directors, Annual Reviews Inc. J. Murray Luck, Founder and Director Emeritus of Annual Reviews Inc.
Professor Emeritus of Chemistry, Stanford University Joshua Lederberg, President of Annual Reviews Inc.
President, The Rockefeller University James E. Howell, Vice President of Annual Reviews Inc.
Professor of Economics, Stanford University Winslow R. Briggs, Director, Carnegie Institution of Washington, Stanford Sidney D. Drell, Deputy Director, Stanford Linear Accelerator Center Sandra M. Faber, Professor of Astronomy, University of California, Santa Cruz Eugene Garfield, President, Institute for Scientific Information William Kaufmann. President, William Kaufmann. Inc. D. E. Koshland, Jr., Professor of Biochemistry, University of California, Berkeley Donald A. B. Lindberg, Director, National Library of Medicine Gardner Lindzey, Director, Center for Advanced Study in the Behavioral Sciences,
Stanford William F. Miller, President, SRI International Charles Yanofsky, Professor of Biological Sciences, Stanford University Richard N. Zare, Professor of Physical Chemistry, Stanford University Harriet A. Zuckerman, Professor of Sociology, Columbia University Management of Annual Reviews Inc. John S. McNeil, Publisher and Secretary-Treasurer William Kaufmann, Editor-in-Chief Mickey G. Hamilton, Promotion Manager Donald S. Svedeman, Business Manager Ann B. McGuire, Production Manager AI'TNUAL REVIEWS OF Anthropology
Medicine
Astronomy and Astrophysics
Microbiology
Biochemistry
Neuroscience
Biophysics and Biophysical Chemistry Cell Bi ology Computer Science
Nuclear and Particle Science Nutrition Pharmacology and Toxicology
Earth and Planetary Sciences
Physical Chemistry
Ecology and Systematics Energy
Physiology Phytopathology
Entomology Fluid Mechanics
Plant Physiology and Plant Molecular Biology Psychology
Genetics Immunology Materials Scie nce
SPECIAL PUBLIGATIONS Excitement and Fascination of Science, Vols I, and 3
2
Intelligence and Affectivity,
by Jean Piaget
Public Health Sociology
A detachable order form/envelope is bound into the back of this volume.
Annu. Rev. Biophys. Biophys. Chern. 1990. 19: l--{j Copyright © 1990 by Annual Reviews Inc. All rights reserved
WHITHER BIOPHYSICS?
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
Gregorio Weber School of Chemical Sciences, University of Illinois, Urbana, Illinois 61801
When I arrived in Cambridge, England from my native Argentina at the end of 1943, I soon visited the famous Cavendish Laboratory. Just before the war, a small detached building had been constructed to house the cryophysics unit that Pieter Kapitza directed previously to his then recent return to Russia. On the outside wall of the building there was a handsome bas-relief of a crocodile by Eric Gill; Kapitza had thought of it as a symbol of science, which, like the crocodile cannot look backwards. When a scientist with many years of experience is asked for a contribution like the present he usually looks back and reminisces over his years, but, in accordance with my crocodilean nature I have chosen to look into the present and future, which in science at least, are usually more interesting ,
than the past. Even if a crocodile cannot look backwards, he may keep some imperfect memories that he can compare with the present and even draw some conclusions about
his
expectations for the future.
The
dominant
impression of this scientist through his years has been the ever-increasing specialization in smaller areas-the atomization of science. This seems the case for every branch of science, but surely the maximum entropy is to be found in biology. By themselves, the biological sciences form the most heterogeneous group of disciplines. Important areas of contact exist with astronomy, geology, physics, chemistry, psychology, and medicine, and no single human mind can knowingly appreciate the arguments or the methodologies that are involved in all thcsc areas of contact. Thus a biologist is necessarily a specialist of some kind, and one who is interested in biophysics is bound to ask two immediate questions: Are there any studies that may be considered central to the understanding of biology? and, What place does biophysics occupy in the confusion of tongues of the Babel of biology? The unique theoretical thread running through the biological sciences is that given by genetics and evolution. Evolution has become the dominant
0883-9182/90/0610-0001$02.00
2
WEBER
idea in biology, and though its connection with genetics was appreciated from the very beginning, it was only with the discovery of the way in which nucleic acids carry and transfer genetic information that the relation between them was clearly formulated. Evolution itself remained a purely formal set of concepts created to explain the diverse animal and plant morphologies of the geological past and the present until the study of bacterial transformations showed how natural selection could be experi
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
mentally tested in the laboratory. Both genetics and evolution had to await the development of biochemistry before they could be formulated in terms of the actual elementary constituents of the organisms and subjected to experimental verification. The definitive proof of the unity of all life on earth has been achieved by the adoption of what we may call, for lack of a better word, the molecular point of view. Its most spectacular triumph has been the practical manipulation of genetic material to change the properties of plant and animal species. Most of us believe that it is from this molecular viewpoint that fresh ideas and new experimental approaches will emerge in the foreseeable future, and it does not appear at all likely that we will see generalizations of first importance in biology derived, like those of Mendel and Darwin, from macroscopic observations. But the molecular point of view, while introducing general rules of analysis and a certain rationalization of the procedures, has not yet resulted in a corresponding increase in conceptual unity. The multiplicity of the subjects of biological research, the complexity and divergent nature of the techniques of investigation that demand intense concentration on particulars, and the almost-exclusive communication of the research bio logist with others who work on precisely the same subject has had as a final result the conversion of the biologist into a specialist, often a narrow one who remains confined to a small scientific territory. This concentration on the limited and the practical needs tQ be balanced by an increasingly more refined analysis and experimental test of the general concepts that form the basis of the many particular studies. Unfortunately, it is easy to notice that while advances that bring practical results are received with enthusiasm and readily embraced, the proposal of new concepts that contradict or modify the old and accepted ones arouse just as much suspicion today as they ever did in the past. In this respect, scientific society has not changed much. The belief that biology is reducible to the properties of matter that physics and chemistry can enumerate has had complete success in practice, but the many new experimental facts thus uncovered have left us orphaned as to theory. Can biophysics provide it? As at present conceived by those that regard themselves as biophysicists biophysics is a very unlikely collection of subjects. The use of physical methodology in biology or medicine is not new. In the nineteenth century
WHITHER BIOPHYSICS?
3
Fick, Poiseuille, and Helmholz made important contributions to classical physics through their interest in the solution of purely biological problems by the use of methods borrowed from physics. We certainly can call them biophysicists, while, at the other extreme, we would hesitate to use this term for anybody who uses a thermometer in his biological research. There is hardly a research subject that one can place exclusively in biophysics. Biophysics is what biophysicists do, but within so much diversity we can
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
distinguish two kinds of biophysicists: Those who research on subjects, in which, at least provisionally, one may ignore the existence of the molecular substratum-systems
biophysicists-and
those
that
may
be
more
properly called molecular biophysicists. As a scientific discipline, systems biophysics is equidistant from bioengineering, which attends to the tech nological imitation or improvement of biological functions, and classical physiology, which formally describes these functions and their inter relations. Though systems biophysics has no easily defined limits and no identifiable general principles, its success in many medical and physio logical applications shows that there are few areas of biology that have not already benefited from such an approach. Molecular biophysics has a more limited but better-defined subject: to interpret in the language of physics and to evaluate by the methods of physics the biological functions at the molecular level. Molecular biophysics presupposes a knowledge of the molecular composition of organisms and the modes of chemical transformation of the molecules in it. In other words, a good working knowledge of the methods and ideas of biochemistry. That molecular biophysics is impossible without biochemistry is demon strated by the changes in our view on the functions of the brain: Not so many years ago the central nervous system was viewed as a kind of telephone central in which the physiological activity could be conceived as resulting solely from the flow of electrical messages from one neuron to another. It was thought then possible to'interpret the nervous activity starting from inhibitory and excitatory electrical properties that required only a physical description. More recently we have learned that the nervous system is the site of a remarkable diversity. The list of neurotransmitters grows larger every year, and the brain is now known to be the most chemically differentiated organ in the body. Thirty years ago when molecular biology began to emerge as an impor tant scientific branch, one could legitimately expect that it would attempt to generalize the various aspects of biology and create from them a unified "exact" science. However molecular biology has taken a very different course and is today, in practice, synonymous with nucleic acid biochem istry, stressing those aspects common to genetics and biochemistry and having as practical aim the manipUlation of genetic material. Interestingly
4
WEBER
enough, the more quantitative physico-chemical aspects of biology receive scant notice in textbooks on molecular biology and in the numerous publications and conferences that concern themselves with the subject. There is, therefore, a need within biology for a discipline that aims at bridging the gap between our knowledge of living organisms as systems and the happenings at the molecular level-in essence, a bridge between systems and molecular biophysics. The isolation of these two branches of
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
biophysics from each other helps to identify what may be called the central problem of biophysics and indeed the central problem of biology: the relation of the microscopic, molecular aspects to the macroscopic functions of organisms. One does not need to read many papers of molecular bio physics to discover that we are virtually helpless in our analysis of any "purposeful" biological function that results from the cooperative inter action of many distinct molecular inputs. Even an apparently simple instance, the folding of a peptide chain into a globular molecule, has defeated all attempts at a molecular reductionist approach, and more complex cases like the motility of various types and the succession of changes involved in cellular and organismic development seem further away from our understanding. All our efforts in these areas are directed to isolate and characterize the molecules present, the implication being that once this is done the rest will follow. We are far from the days when Boltzman had difficulty in convincing other scientists of the merits of the molecular approach and we have come to disregard, or rather to take for granted, the fundamental importance of the macroscopic point of view as taught to us by thermodynamics. By employing the essentially macroscopic chemistry of Lavoisier and the equally macroscopic energetics of Gibbs we can predict, from their chemical potential differences, the direction and extent of many chemical reactions even when the energetic changes involve only fractions of a kilocalorie. Yet we cannot, and we are not even close to, predict these by appeal to microscopic molecular theory. Our deficiencies in this area have been not so much helped as revealed by the advances in numerical computation. The use of digital computers has pcrmitted us to enormously improve the reliability in the quantitative analysis of phenomena of almost any kind. At the same time, it has helped the techniques of chemical analysis to demonstrate the existence of an enormous diversity at the molecular level, a diversity that continues to grow with every improvement in resolution of those techniques. The dis covery of so much complexity has lead many to despair about the prospects of a reductionist molecular approach to the phenomena of biology. We seem to be defeated not so much by our ignorance of the underlying physical and chemical properties as by the difficulties of combining them to obtain a final result.
WHITHER BIOPHYSICS?
5
The first step in the reductionist ascent from the microscopic to the macroscopic, the prediction of macromolecular�particularly protein� structurc has proven difficult. We no longer aim at dcducing protein structure from simple amino acid sequences, as was attempted in the first flush of computational enthusiasm. More modestly, we propose to take the structures given to us by the X-ray crystallographers and to explain their stability and their very short term dynamics. The results are more
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
interesting for the demonstration of the limitations of our present com putational methods and the difficulties of the reductionist approach than for any insight into the physics of macromolecules. The causes of these shortcomings are interesting in that they may furnish us with ways of doing better in the future. It seems indeed surprising that we are attempting to apply a few rules regarding atomic interactions, whose generality may be questioned, to something as complicated as a globular protein without clear indication that these rules yield the correct answers when applied to much simpler systems, e.g. micromolecular complexes, in solution. I have often mused about the application of simpleminded macroscopic
electrostatics to molecules of all kinds. Protonated lysine and arginine must be completely equivalent in their electrostatic effects yet the free energy of neutralization of both differ by more than 3 kcal/mol. Should we not try to understand how these differences arise and how they modify the association of small molecules in solution before we attempt cal culations in a protein? And this is only one of many difficulties: Can we take for granted that the various types of atomic interactions (London van der Waals, electrically induced and permanent-charge interactions) are without influence upon each other and should simply be added up? In the examination of the very simplest cases we may be able to reach a decision on these and other dubious points but in the case of a protein in which hundreds of interactions balance each other to yicld a resultant in free energy of only a few kilocalories, the chances of reaching unequivocal conclusions, or even estimates, on the suitability of this or that initial assumption are zero. Besides, the multiplicity of interactions themselves requires an increase in the precision of the parameters associated with them as the number of the elements involved in the calculation (atoms, groups, etc.) increases. It is horrifying to think what it must be for the simplest protein, but I have yet to see an estimate of the probable errors that must arise from this cause in computations of the molecular dynamics of proteins. Of course, all these difficulties are mitigated by the fact that one knows in advance the result that one must get, and then it is not so difficult to reach agreement with expectations. I am not implying any actual voluntary forcing of the results. In doing computations infinitely less complicated than those that involve a protein, "atom by atom," I (and
6
WEBER
surely many others) have become struck by the frequcncy with which one makes compensating mistakes and obtains something that looks quite acceptable until.
.
.
.
Before I lose any more friends, let me assure them
that I greatly admire thc practitioners of these "supercomputations" for their bravery, that I share their views on the importance of the subject, and that I listen enraptured to their presentations (particularly those in color), though hoping always for something less exalted but closer to my
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
limited understanding. The failure of the molecular computations that jump from the atom to the protein without passing through less complicated molecules, should warn us of the futility of a reductionism that attempts to directly link the atomic to the macroscopic. Reductionism can get a bad name if it aims, as Truesdell has put it, "to explain the behaviour of the rat starting with the equations of motion of the rat particles." Many intermediate stages are required and at each of these stages we learn the new things that the elementary properties imply, without ever being able to deduce the new from the well known without some help from reality. There is a very large gap yet between the properties of atoms and small molecules and those of the biological systems. To bridge it will require beginning with a thorough examination, both experimental and theoretical, of the simplest molecular associations in solution. It is a pity that there are so few biochemists and physical chemists who are attempting to tackle this unglamorous, but highly promising and absolutely necessary, subject. I will be more than pleased if this article draws some able young man into these studies. When I started to be interested in molecular complexes�not very long after my visit to the Cavendish Laboratory�it seemed that from them to the proteins it was but a small step. Everything has turned out to be much more complicated than what I, and probably most others, expected, and we still have not reached to the end of the molecular complexities that make for the entertaining diversity of life. However, these complexities need not be infinite, and if we build consistently from both ends, the macroscopic-thermodynamic end and the microscopic-molecular end, we may find one of these days that a general understanding of biology in terms of molecular properties is not so impossible or distant as it now appears.
ANNUAL REVIEWS
Quick links to online content
Further
ANNUAL REVIEWS INC. is a nonprofit scientific publisher established to promote the advancement of the sciences. Beginning in 1932 with the Annual Review
of Biochemistry, the Company has pursued as its principal function the publication of high quality, reasonably priced Annual Review volumes. The volumes are organized by Editors and Editorial Committees who invite qualified authors to contribute critical articles reviewing significant developments within each major discipline. The Editor-in-Chief invites those interested in serving as future Editorial Committee members to communicate directly with him. Annual Reviews Inc. is administered by a Board of Directors, whose members serve without compensation.
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
1990 Board of Directors, Annual Reviews Inc. J. Murray Luck, Founder and Director Emeritus of Annual Reviews Inc.
Professor Emeritus of Chemistry, Stanford University Joshua Lederberg, President of Annual Reviews Inc.
President, The Rockefeller University James E. Howell, Vice President of Annual Reviews Inc.
Professor of Economics, Stanford University Winslow R. Briggs, Director, Carnegie Institution of Washington, Stanford Sidney D. Drell, Deputy Director, Stanford Linear Accelerator Center Sandra M. Faber, Professor of Astronomy, University of California, Santa Cruz Eugene Garfield, President, Institute for Scientific Information William Kaufmann. President, William Kaufmann. Inc. D. E. Koshland, Jr., Professor of Biochemistry, University of California, Berkeley Donald A. B. Lindberg, Director, National Library of Medicine Gardner Lindzey, Director, Center for Advanced Study in the Behavioral Sciences,
Stanford William F. Miller, President, SRI International Charles Yanofsky, Professor of Biological Sciences, Stanford University Richard N. Zare, Professor of Physical Chemistry, Stanford University Harriet A. Zuckerman, Professor of Sociology, Columbia University Management of Annual Reviews Inc. John S. McNeil, Publisher and Secretary-Treasurer William Kaufmann, Editor-in-Chief Mickey G. Hamilton, Promotion Manager Donald S. Svedeman, Business Manager Ann B. McGuire, Production Manager AI'TNUAL REVIEWS OF Anthropology
Medicine
Astronomy and Astrophysics
Microbiology
Biochemistry
Neuroscience
Biophysics and Biophysical Chemistry Cell Bi ology Computer Science
Nuclear and Particle Science Nutrition Pharmacology and Toxicology
Earth and Planetary Sciences
Physical Chemistry
Ecology and Systematics Energy
Physiology Phytopathology
Entomology Fluid Mechanics
Plant Physiology and Plant Molecular Biology Psychology
Genetics Immunology Materials Scie nce
SPECIAL PUBLIGATIONS Excitement and Fascination of Science, Vols I, and 3
2
Intelligence and Affectivity,
by Jean Piaget
Public Health Sociology
A detachable order form/envelope is bound into the back of this volume.
Annu. Rev. Biophys. Biophys. Chern. 1990. 19: l--{j Copyright © 1990 by Annual Reviews Inc. All rights reserved
WHITHER BIOPHYSICS?
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
Gregorio Weber School of Chemical Sciences, University of Illinois, Urbana, Illinois 61801
When I arrived in Cambridge, England from my native Argentina at the end of 1943, I soon visited the famous Cavendish Laboratory. Just before the war, a small detached building had been constructed to house the cryophysics unit that Pieter Kapitza directed previously to his then recent return to Russia. On the outside wall of the building there was a handsome bas-relief of a crocodile by Eric Gill; Kapitza had thought of it as a symbol of science, which, like the crocodile cannot look backwards. When a scientist with many years of experience is asked for a contribution like the present he usually looks back and reminisces over his years, but, in accordance with my crocodilean nature I have chosen to look into the present and future, which in science at least, are usually more interesting ,
than the past. Even if a crocodile cannot look backwards, he may keep some imperfect memories that he can compare with the present and even draw some conclusions about
his
expectations for the future.
The
dominant
impression of this scientist through his years has been the ever-increasing specialization in smaller areas-the atomization of science. This seems the case for every branch of science, but surely the maximum entropy is to be found in biology. By themselves, the biological sciences form the most heterogeneous group of disciplines. Important areas of contact exist with astronomy, geology, physics, chemistry, psychology, and medicine, and no single human mind can knowingly appreciate the arguments or the methodologies that are involved in all thcsc areas of contact. Thus a biologist is necessarily a specialist of some kind, and one who is interested in biophysics is bound to ask two immediate questions: Are there any studies that may be considered central to the understanding of biology? and, What place does biophysics occupy in the confusion of tongues of the Babel of biology? The unique theoretical thread running through the biological sciences is that given by genetics and evolution. Evolution has become the dominant
0883-9182/90/0610-0001$02.00
2
WEBER
idea in biology, and though its connection with genetics was appreciated from the very beginning, it was only with the discovery of the way in which nucleic acids carry and transfer genetic information that the relation between them was clearly formulated. Evolution itself remained a purely formal set of concepts created to explain the diverse animal and plant morphologies of the geological past and the present until the study of bacterial transformations showed how natural selection could be experi
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
mentally tested in the laboratory. Both genetics and evolution had to await the development of biochemistry before they could be formulated in terms of the actual elementary constituents of the organisms and subjected to experimental verification. The definitive proof of the unity of all life on earth has been achieved by the adoption of what we may call, for lack of a better word, the molecular point of view. Its most spectacular triumph has been the practical manipulation of genetic material to change the properties of plant and animal species. Most of us believe that it is from this molecular viewpoint that fresh ideas and new experimental approaches will emerge in the foreseeable future, and it does not appear at all likely that we will see generalizations of first importance in biology derived, like those of Mendel and Darwin, from macroscopic observations. But the molecular point of view, while introducing general rules of analysis and a certain rationalization of the procedures, has not yet resulted in a corresponding increase in conceptual unity. The multiplicity of the subjects of biological research, the complexity and divergent nature of the techniques of investigation that demand intense concentration on particulars, and the almost-exclusive communication of the research bio logist with others who work on precisely the same subject has had as a final result the conversion of the biologist into a specialist, often a narrow one who remains confined to a small scientific territory. This concentration on the limited and the practical needs tQ be balanced by an increasingly more refined analysis and experimental test of the general concepts that form the basis of the many particular studies. Unfortunately, it is easy to notice that while advances that bring practical results are received with enthusiasm and readily embraced, the proposal of new concepts that contradict or modify the old and accepted ones arouse just as much suspicion today as they ever did in the past. In this respect, scientific society has not changed much. The belief that biology is reducible to the properties of matter that physics and chemistry can enumerate has had complete success in practice, but the many new experimental facts thus uncovered have left us orphaned as to theory. Can biophysics provide it? As at present conceived by those that regard themselves as biophysicists biophysics is a very unlikely collection of subjects. The use of physical methodology in biology or medicine is not new. In the nineteenth century
WHITHER BIOPHYSICS?
3
Fick, Poiseuille, and Helmholz made important contributions to classical physics through their interest in the solution of purely biological problems by the use of methods borrowed from physics. We certainly can call them biophysicists, while, at the other extreme, we would hesitate to use this term for anybody who uses a thermometer in his biological research. There is hardly a research subject that one can place exclusively in biophysics. Biophysics is what biophysicists do, but within so much diversity we can
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
distinguish two kinds of biophysicists: Those who research on subjects, in which, at least provisionally, one may ignore the existence of the molecular substratum-systems
biophysicists-and
those
that
may
be
more
properly called molecular biophysicists. As a scientific discipline, systems biophysics is equidistant from bioengineering, which attends to the tech nological imitation or improvement of biological functions, and classical physiology, which formally describes these functions and their inter relations. Though systems biophysics has no easily defined limits and no identifiable general principles, its success in many medical and physio logical applications shows that there are few areas of biology that have not already benefited from such an approach. Molecular biophysics has a more limited but better-defined subject: to interpret in the language of physics and to evaluate by the methods of physics the biological functions at the molecular level. Molecular biophysics presupposes a knowledge of the molecular composition of organisms and the modes of chemical transformation of the molecules in it. In other words, a good working knowledge of the methods and ideas of biochemistry. That molecular biophysics is impossible without biochemistry is demon strated by the changes in our view on the functions of the brain: Not so many years ago the central nervous system was viewed as a kind of telephone central in which the physiological activity could be conceived as resulting solely from the flow of electrical messages from one neuron to another. It was thought then possible to'interpret the nervous activity starting from inhibitory and excitatory electrical properties that required only a physical description. More recently we have learned that the nervous system is the site of a remarkable diversity. The list of neurotransmitters grows larger every year, and the brain is now known to be the most chemically differentiated organ in the body. Thirty years ago when molecular biology began to emerge as an impor tant scientific branch, one could legitimately expect that it would attempt to generalize the various aspects of biology and create from them a unified "exact" science. However molecular biology has taken a very different course and is today, in practice, synonymous with nucleic acid biochem istry, stressing those aspects common to genetics and biochemistry and having as practical aim the manipUlation of genetic material. Interestingly
4
WEBER
enough, the more quantitative physico-chemical aspects of biology receive scant notice in textbooks on molecular biology and in the numerous publications and conferences that concern themselves with the subject. There is, therefore, a need within biology for a discipline that aims at bridging the gap between our knowledge of living organisms as systems and the happenings at the molecular level-in essence, a bridge between systems and molecular biophysics. The isolation of these two branches of
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
biophysics from each other helps to identify what may be called the central problem of biophysics and indeed the central problem of biology: the relation of the microscopic, molecular aspects to the macroscopic functions of organisms. One does not need to read many papers of molecular bio physics to discover that we are virtually helpless in our analysis of any "purposeful" biological function that results from the cooperative inter action of many distinct molecular inputs. Even an apparently simple instance, the folding of a peptide chain into a globular molecule, has defeated all attempts at a molecular reductionist approach, and more complex cases like the motility of various types and the succession of changes involved in cellular and organismic development seem further away from our understanding. All our efforts in these areas are directed to isolate and characterize the molecules present, the implication being that once this is done the rest will follow. We are far from the days when Boltzman had difficulty in convincing other scientists of the merits of the molecular approach and we have come to disregard, or rather to take for granted, the fundamental importance of the macroscopic point of view as taught to us by thermodynamics. By employing the essentially macroscopic chemistry of Lavoisier and the equally macroscopic energetics of Gibbs we can predict, from their chemical potential differences, the direction and extent of many chemical reactions even when the energetic changes involve only fractions of a kilocalorie. Yet we cannot, and we are not even close to, predict these by appeal to microscopic molecular theory. Our deficiencies in this area have been not so much helped as revealed by the advances in numerical computation. The use of digital computers has pcrmitted us to enormously improve the reliability in the quantitative analysis of phenomena of almost any kind. At the same time, it has helped the techniques of chemical analysis to demonstrate the existence of an enormous diversity at the molecular level, a diversity that continues to grow with every improvement in resolution of those techniques. The dis covery of so much complexity has lead many to despair about the prospects of a reductionist molecular approach to the phenomena of biology. We seem to be defeated not so much by our ignorance of the underlying physical and chemical properties as by the difficulties of combining them to obtain a final result.
WHITHER BIOPHYSICS?
5
The first step in the reductionist ascent from the microscopic to the macroscopic, the prediction of macromolecular�particularly protein� structurc has proven difficult. We no longer aim at dcducing protein structure from simple amino acid sequences, as was attempted in the first flush of computational enthusiasm. More modestly, we propose to take the structures given to us by the X-ray crystallographers and to explain their stability and their very short term dynamics. The results are more
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
interesting for the demonstration of the limitations of our present com putational methods and the difficulties of the reductionist approach than for any insight into the physics of macromolecules. The causes of these shortcomings are interesting in that they may furnish us with ways of doing better in the future. It seems indeed surprising that we are attempting to apply a few rules regarding atomic interactions, whose generality may be questioned, to something as complicated as a globular protein without clear indication that these rules yield the correct answers when applied to much simpler systems, e.g. micromolecular complexes, in solution. I have often mused about the application of simpleminded macroscopic
electrostatics to molecules of all kinds. Protonated lysine and arginine must be completely equivalent in their electrostatic effects yet the free energy of neutralization of both differ by more than 3 kcal/mol. Should we not try to understand how these differences arise and how they modify the association of small molecules in solution before we attempt cal culations in a protein? And this is only one of many difficulties: Can we take for granted that the various types of atomic interactions (London van der Waals, electrically induced and permanent-charge interactions) are without influence upon each other and should simply be added up? In the examination of the very simplest cases we may be able to reach a decision on these and other dubious points but in the case of a protein in which hundreds of interactions balance each other to yicld a resultant in free energy of only a few kilocalories, the chances of reaching unequivocal conclusions, or even estimates, on the suitability of this or that initial assumption are zero. Besides, the multiplicity of interactions themselves requires an increase in the precision of the parameters associated with them as the number of the elements involved in the calculation (atoms, groups, etc.) increases. It is horrifying to think what it must be for the simplest protein, but I have yet to see an estimate of the probable errors that must arise from this cause in computations of the molecular dynamics of proteins. Of course, all these difficulties are mitigated by the fact that one knows in advance the result that one must get, and then it is not so difficult to reach agreement with expectations. I am not implying any actual voluntary forcing of the results. In doing computations infinitely less complicated than those that involve a protein, "atom by atom," I (and
6
WEBER
surely many others) have become struck by the frequcncy with which one makes compensating mistakes and obtains something that looks quite acceptable until.
.
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Before I lose any more friends, let me assure them
that I greatly admire thc practitioners of these "supercomputations" for their bravery, that I share their views on the importance of the subject, and that I listen enraptured to their presentations (particularly those in color), though hoping always for something less exalted but closer to my
Annu. Rev. Biophys. Biophys. Chem. 1990.19:1-8. Downloaded from www.annualreviews.org Access provided by 117.253.156.67 on 11/11/15. For personal use only.
limited understanding. The failure of the molecular computations that jump from the atom to the protein without passing through less complicated molecules, should warn us of the futility of a reductionism that attempts to directly link the atomic to the macroscopic. Reductionism can get a bad name if it aims, as Truesdell has put it, "to explain the behaviour of the rat starting with the equations of motion of the rat particles." Many intermediate stages are required and at each of these stages we learn the new things that the elementary properties imply, without ever being able to deduce the new from the well known without some help from reality. There is a very large gap yet between the properties of atoms and small molecules and those of the biological systems. To bridge it will require beginning with a thorough examination, both experimental and theoretical, of the simplest molecular associations in solution. It is a pity that there are so few biochemists and physical chemists who are attempting to tackle this unglamorous, but highly promising and absolutely necessary, subject. I will be more than pleased if this article draws some able young man into these studies. When I started to be interested in molecular complexes�not very long after my visit to the Cavendish Laboratory�it seemed that from them to the proteins it was but a small step. Everything has turned out to be much more complicated than what I, and probably most others, expected, and we still have not reached to the end of the molecular complexities that make for the entertaining diversity of life. However, these complexities need not be infinite, and if we build consistently from both ends, the macroscopic-thermodynamic end and the microscopic-molecular end, we may find one of these days that a general understanding of biology in terms of molecular properties is not so impossible or distant as it now appears.
