Abstract
The conference 'From DNA-Inspired Physics to Physics-Inspired Biology' (1–5 June 2009, International Center for Theoretical Physics, Trieste, Italy) that myself and two former presidents of the American Biophysical Society—Wilma Olson (Rutgers University) and Adrian Parsegian (NIH), with the support of an ICTP team (Ralf Gebauer (Local Organizer) and Doreen Sauleek (Conference Secretary)), have organized was intended to establish stronger links between the biology and physics communities on the DNA front. The relationships between them were never easy. In 1997, Adrian published a paper in Physics Today ('Harness the Hubris') summarizing his thoughts about the main obstacles for a successful collaboration. The bottom line of that article was that physicists must seriously learn biology before exploring it and even having an interpreter, a friend or co-worker, who will be cooperating with you and translating the problems of biology into a physical language, may not be enough. He started his story with a joke about a physicist asking a biologist: 'I want to study the brain. Tell me something about it!' Biologist: 'First, the brain consists of two parts, and..' Physicist: 'Stop. You have told me too much.'
Adrian listed a few direct avenues where physicists' contributions may be particularly welcome. This gentle and elegantly written paper caused, however, a stormy reaction from Bob Austin (Princeton), published together with Adrian's notes, accusing Adrian of forbidding physicists to attack big questions in biology straightaway. Twelve years have passed and many new developments have taken place in the biologist–physicist interaction. This was something I addressed in my opening conference speech, with my position lying somewhere inbetween Parsegian's and Austin's, which is briefly outlined here. I will first recall certain precepts or 'dogmas' that fly in the air like Valkyries, poisoning those relationships.
Since the early seventies when I was a first year PhD student at the Frumkin Institute in Moscow attending hot theoretical seminars chaired by Benjamin Levich (1917–1986, a pupil of Landau and the founding father of physical–chemical hydrodynamics), I particularly remember one of his many jokes he used to spice up his seminar. When some overly enthusiastic speaker was telling us with 100% confidence how the electron transfers between atomic moieties in a solvent near an electrode, and what the molecules exactly do to promote the transfer, he used to ask the speaker: 'How do you know it? Have you been there?'
Today this is no longer a question or even a joke. We have plenty of experimental tools to 'get there'. The list of such techniques is too long to cover fully, I may just refer to FIONA (fluorescence imaging with nanometer accuracy) which allows us to trace the motion of myosin on actin or kinesin on microtubules and similar aspects of protein motility in vivo and in vitro (fluorescence methods were at the center of the Biological and Molecular Machine Program at Kavli ITP, Santa Barbara, where the founders of those techniques taught us what we can learn using them) or visualizing the positions of adsorbed counterions on DNA by synchrotron radiation. Therefore, the following dogmas can be given:
Dogma 1: 'Seeing is believing'. Once, I asked an Assistant Professor from one of the top US universities, who was preaching such methods, had he tried to plot his data in some coordinates, where I would have expected his data to lie on a straight line. The answer was, 'Come on, what you speak about is 20th century science; it's no longer interesting!' I am afraid he was not unique in his generation, voting for what I would call 'MTV-science'. This science does make you dance, but on its own is not sufficient without a deep theoretical analysis of what you actually see. Otherwise, 'what you see is what you get' and not more.
Dogma 2: 'A theory must contain not more than exponential functions, logarithms and alike. Otherwise the job should be left with computers. No Bessel functions, please!' This point of view was advocated by my office mate at KITP, Rob Philips, Professor of Applied Physics and Molecular Biophysics at Caltech, who found his new love—biology: from solid state theory. We had heated arguments about it. And my strongest one was that it was the maths of the now famous paper by Cochran et al [1] that allowed Watson and Crick to decipher the DNA x-ray patterns of Rosalind Franklin. The CCV formula for the x-ray scattering intensity fully explained the structure of the famous cross of the scattering maxima on the (kz, K)-map, where kz and K are, respectively, the components of the scattering wave-vector transfer in the direction along the main axis of the columnar array of the DNA molecules and in the perpendicular plane. From the distance and the position of the darkest spots on that pattern it was possible to deduce that the studied DNA has a shape of a double helix, to find its radius, the width of the minor and major groove, the vertical rise between base pairs, and the helical pitch. There were still some features in that pattern which have not been noticed, which were only understood half a century later after the corresponding extension of the CCV theory [2, 3], but those were not essential for solving the structure of DNA itself at that time, but rather for the understanding of DNA–DNA interactions and their effect on more subtle aspects of DNA structure, which are an issue today. The 'Bessel function' was the key player in the CCV equation and the extensions that followed.
Dogma 3:'This happened once. It is unlikely to ever happen again' (from a conversation with a respectable editor of a high-profile biological journal about the revolution made by physics in biology). This is a common opinion, at least in the biological community. Note, that of the four discoverers of the DNA structure, three were physicists and only Watson was a biologist, and the key secret in that discovery was the 'chemistry' between an enthusiastic biologist (Watson) and physicist (Crick) that helped them to find common language, and as a result discover not only the structure but also the 'function' of DNA. Now we know that the machinery of DNA replication is very complex, promoted by motor proteins such as DNA helicase, polymerase, ligases etc, but the complementary principle of synthesis of two identical DNA molecules on the unwound complimentary single strands as templates remains the same as mentioned in the famous phrase ('It did not escape our attention') of the first Watson–Crick paper.
Dogma 4: (Almost literally from a letter from Don Roy Forsdyke, Biochemistry Professor at Queens Ontario). 'Biologists will not read a paper with formulae. The biological literature is vast. Biologists have too many papers to read and too many experiments to make. They will leave aside any reading that looks difficult'. If this is true, and I think it is, we are in big trouble; this brings us to the next dogma.
Dogma 5: (Catch 22) It is impossible to publish a serious theoretical paper in a biological journal. Physicists, particularly, theorists need derivations to prove the validity of their findings. But with the derivations in the script, the paper will be rejected. If you still publish it in a physical journal it will not be read by those to whom it is addressed.
Dogma 6:Physicists are too ignorant to offer biologists anything useful. Perhaps, some new spectroscopic method or apparatus for force measurement, but that's about it. Leave biology to professionals. Full stop. I make no comments about this extreme point of view, referring the reader to the dispute between Parsegian and Austin, which is still quite relevant today.
Next, a pearl of wisdom of a theoretical physicist, Nobel Laureate in Physiology and Medicine, Max Delbrück (Caltech), formulated in his 1949 lecture in Copenhagen, the principles on which organisms of today are based must have been determined by a couple of billion years of evolutionary history; 'you cannot expect to explain so wise an old bird in a few simple words'. It is indisputably so, but it is followed by two other competing sub-dogmas:
Dogma N6a: Physics wants to simplify and unify things, as much as possible, biology resists the reductionist approach and is happy about diversification and complexity.
In my opinion all these dogmas have been beaten by this icon, the understanding of which gave rise to the idea of DNA replication and all the following principles of molecular biology. Not only 'this will happen again' but on a smaller scale this happens all the time.
Generally, through centuries, physics and mathematics have changed our lives completely. In a short article one cannot give a full list of such achievements from Aristotle's time, but I name just a few of the summits of the last two centuries. A great physicist Rutherford (who was, by the way, a Nobel Laureate in Chemistry for 'his investigations into the disintegration of the elements, and the chemistry of radioactive substances') was also famous for an extreme (and definitely outdated) statement: 'All science is either stamp collecting or physics'. Let us paraphrase him and collect some stamps.
I have no space to stop on the Faraday–Ampere laws of stationary electricity (who cares, electric current comes from a plug would be the answer of most of people unfamiliar with physics, and forget about electricity that is supplied to biological laboratories). So, let us go straight away to James Clerk Maxwell. He derived four equations that related electricity and magnetism and, as the legend tells us, it took him seven years to write the fourth equation to complete the set with four unknown variables. The story of the fourth Maxwell equation is one of the most dramatic stories in the history of science [4]. As a solution of that set he obtained relativistically-invariant electromagnetic waves, which no one saw and the consequences of which no one had foreseen at that time. But very soon Hertz understood how to generate them, Thomson how to receive them, and now we have the world all connected online.
My next stamp goes to the Zhukovski equation of the hydrodynamics of a wing, which explained how aerodynamic lift force is generated. Now we can get from London to Washington in a third of a day, essentially due to that equation.
Of the many things that the genius of Einstein discovered his energy-matter relation has led us to atomic power, whether we like it or not.
Rutherford and Bohr unraveled the structure of atoms and all our materials science followed from it.
Discovery of the transistor made the world of electronics and computers possible, and, again—whether we like it or not—most of us spend many hours daily staring at computer screens.
Crick's equations and Franklin–Wilkins' observations (made possible by Roentgen's discovery that I omitted to mention after Maxwell) gave rise to the world of molecular biology which could also be easily forgotten by the wide public, if not our ever grateful forensic experts.
Just two more milestones of much more 'modest' caliber. This is the discovery of lasers which are massively used for communication, in medicine and spectroscopy, including biological research. Next, I mention the discovery of scanning probe techniques, which allowed us to see individual atoms. For these two I did not even find stamps, but I am sure they must exist somewhere. The STM has just led Stuart Lindsey's team (University of Arizona) to the first steps towards ultrafast sequencing of DNA using functionalized STM tips.
At the Abdus Salam International Center for Theoretical Physics there is no need to convince anyone that involved mathematics and physics is needed. But neither do we need to explain to anyone there that the applications of physics may be equally exciting as its fundamentals. The appreciation of massive achievements of physical methods in DNA research made it possible to host and massively sponsor this DNA conference at the ICTP. The conference was generously co-sponsored by the Wellcome Trust (UK). It comprised approximately 60 talks on topically focused sessions devoted to:
DNA mechanics
DNA structure, interactions and aggregation
Recognition of homologous genes
Conformational dynamics, supercoiling and packing
DNA compactization in viruses
DNA-protein interaction and recognition
DNA in confinement (pores and vesicles)
Smart DNA (robotics, nano-architectures, switches, sensors and DNA electronics)
The success of the conference was that it was not a meeting of a club of physicists interested in biology, but a meeting of physicists, carrying out important work widely published not only in physical but also biological journals, with the leading biologists who, personally, were keenly interested in learning what novelties physical methods and existing knowledge could offer them. They were equally eager to explain to physicists and mathematicians the most challenging paradigms of molecular biology research. The conference was opened by two inspiring high-impact talks, from a Director of the European Molecular Genetics Center in Trieste, Arturo Falaschi, the Editor of HFSP Journal (who sadly just passed away last month), and from a scientist of the next generation, Lynn Zechiedrich, Professor of Baylor Medical School and former co-worker of the late Nick Cozzarelly. Both showed astounding manifestations of the polymeric behavior of DNA, where physics is eagerly awaited like rain in the desert. However, at the whole conference about 40% of lectures were delivered by biologists. In this short article it is not possible to cover even the most exciting presentations, and I refer interested readers to the website [5] where further information can be found. I will outline below just a couple of issues.
The conference revealed big progress in understanding the details of DNA mechanics, including its local sequence-dependent elastic properties. Progress was achieved in understanding the role of electrostatic interactions with ions and charged moieties that can influence the shape and elasticity of DNA, highlighted particularly in the studies of Jim Maher (University of Minnesota). Generally, the role of helical structure dependent, so called `helix-specific' interactions on which the lecture of Sergey Leikin (NIH) was focused, was unequivocally found to play a crucial role in the interaction, aggregation and assembly of DNA—from liquid crystals to intracellular compartments, as well as viral capsids.
One of the hottest sessions was devoted to the 'last great enigma' of genetic recombination: its 'zero' stage—the recognition of homologous genes. The big picture was overviewed in biological terms by Adi Barzel (following a 'manifesto' article with Martin Kupiec [6]). New experiments were then reported that showed that DNA can recognize its homology from a distance without unzipping and local base pair formation. The reported published experiments of an Imperial-NIH team [7], widely discussed last year under a controversial notion of DNA-'telepathy' (in quotes, of course), were based on the direct observation of spontaneous segregation of homologous DNA in cholesteric liquid crystals. The reported by Mara Prentiss, and now published, beautiful experiments of the Harvard team [8] were more involved and were based on the application of the magnetic bead technique (purely physical methods). These have unambiguously demonstrated homology pairing at the double-stranded DNA level, also providing evidence of unimportance of defect-based Watson and Crick pairing in this phenomenon. Both kinds of experiments supported the expectations of an electrostatic snapshot recognition mechanism behind intact, double-stranded DNA homology pairing [9]. But none of them has yet systematically studied its various features, after which one could consider the mentioned mechanism experimentally confirmed. Discussions at breakout meetings referred to the experiments to be performed, that might finally rebute the last presumption of molecular biology that only Watson and Crick pairing can provide recognition, i.e. that the recognition between intact double stranded DNA is impossible. Notably the suggested electrostatic snap-shot recognition mechanism is also based on the helical structure of DNA and correlation of the structure with the text of the sequence (for further details see [10].)
DNA packing in chromatin and chromatin dynamics were the main focus of the conference. Andrew Travers (Ecole Normale Superiore de Cachan), exposed the problem in all its biological complexity, followed by the physical insight into its modeling, overviewed by Helmut Schiessel. Using different kinds of single molecule pulling experiments Jörge Langowski (University of Heidelberg) and David Bensimon (Laboratoire Physique Statistique, Paris) revealed invaluable insights into nucleosome opening and the role of remodeling factors. Jim Kadonaga (UCSD) reported a discovery of a new ATP driven motor-protein, exhibiting annealing/reverse helicase activity. Lars Nordensiöld (Singapore Nanyang TU) has established the sequence of counterions promoting DNA compactization in chromatin, and so on.
Another class of astounding results was related with the structure of DNA phases, coils and toroids in viral capcids, understanding of which at the nanoscopic level, is instrumental for the development of antiviral therapies. Bill Gelbart (UCLA) and Avi Ben-Shaul (Hebrew University of Jerusalem) highlighted various aspects of packing inside the capsids, as well as how viral DNA or RNA can get in and out. Amazing observations of Francoise Livolant have shown the local liquid crystalline structure of DNA in that dense packing. The experiments of her group have unambiguously demonstrated azimuthal correlations between the densely packed double strands, in agreement with similar effects detected earlier in wet DNA fibers described on the physical level in the talk of Sergey Leikin [11].
No matter which aspect of DNA research was discussed at the conference, the physical chemistry of solution, particularly the role of counterions, was found to be extraordinarily important. Loren Williams (Georgia Tech) presented decisive synchrotron x-ray 3d-maps of distribution of the most important class of adsorbed counterions between the major and minor grooves of DNA or phosphates. Purely physical methods were used to obtain them with the results crucial for understanding the resulting charge patterns of DNA (including the adsorbed counterions) that determine DNA physical behaviour and DNA–DNA helix specific forces.
The conference has shown substantial progress in the characterization, understanding of physics, geometry and topology of DNA-supercoiling, as well as its biological implementations, and a set of lectures was devoted to its modeling and experimental characterization.
New techniques were also the center of attention, such as DNA transport through solid-state pores. In particular, Serge Lemay (Kavli Institute, TU Delft, now at Twente) has shown a number of new developments related to a combination of magnetic tweezers techniques and transport, allowing him to precisely characterize the trapping of DNA in the pores and revealing what can be learned from it. Amit Meller (BU) reported an intriguing result showing that DNA capture rate increases with its length for medium long DNA whereas there is no length dependence for longer molecules. Statistical physics of polymers was needed to explain this, revealing also a crucial role of electrostatics. Creation of salt gradients across the pore is providing a tool that increases the sensitivity of this popular new method by an order of magnitude. A unique single molecule technique to study the effect of RNA polymeraze backtracking, using a dual trap optical tweezers assay, was reported by Stephan Grill (Max-Plank Institute, Dresden).
Many theoretical models reported at the conference were elegant, but most importantly closely related to experimental findings.
On the first day of the meeting we were able to celebrate Adrian Parsegian's 70th birthday. A worldwide renowned figure in modern biological physics, its distinguished veteran, a former President of the Biophysical Society and an author of many seminal, pioneering papers, Adrian has worked at the NIH for four decades and over the last two has led a vibrant Structural and Physical Biology Laboratory, created by him. Adrian has done a lot for physicists and biologists coming closer together. That summer, full of his ever young energy—an example for many young scientists—he is moving to build a new research team as a Professor at the University of Massachusetts at Amherst.
My feeling is that something is beginning to move in the difficult interactions between the physical and biological communities, the progress noticeable at least at the scale of 130 people present in Trieste. A few years ago, Paul Selvin, a biophysicist at the University of Illinois who has made crucial contributions to the visualization and characterization of biomolecular motility, suggested that if Rutherford was alive today, he would have possibly conclude that 'All science is either....biology or tool-making for biology... or not fundable'. Generally, 'pride and prejudice' today is no longer on the side of physicists. But in order to overcome the barrier of skepticism we, physicists, not only should not be shy about what we were able to demonstrate in the test tube, but also have to think how we could show that our 'beautiful physical effects' work equally inside the cell! This is much more difficult.
Many of us will not be able to do it alone without finding a biologist match. Crick was not only a great mind, he was also lucky to meet his biologist. But Crick himself was very serious about real biology rather than just 'biologically-inspired physics'. And this is what Adrian advised all of us to do in his 1997 Physics Today paper. But in support of his opponent, Bob Austin, I wish to quote the conclusion from a memorable Steven Hawking's talk at the White House: 'The greatest discoveries of the 21st century will be, where we don't expect them'. So, physics will bring surprises to biology, and the conference left us no doubt of it.
Acknowledgments
I wish to thank John Seddon (Imperial College, UK) for useful remarks about these comments. The initial version of this article featured a collection of post stamps/photos, illustrating the discoveries mentioned in it. As it was difficult to obtain permissions to reproduce these pictures in print, we had to delete all of them, at the last moment. I apologize for this, but although the presentation became less flashy, I still think that the arguments remained clear. There is therefore nobody to acknowledge on this front.
References
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[5] http://cdsagenda5.ictp.trieste.it/full_display.php?ida=a08164
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