Bernie Yurke

Bernie Yurke has a PhD in Physics from Cornell University, and a BS and an MA, both in Physics from the University of Texas at Austin. He started working at Bell Labs in 1982. He has performed research in the areas: force generation of microtubules, phase-ordering kinetics in liquid crystals, and squeezed state generation at optical and microwave frequencies. His current research focuses on self-assembly using DNA. Bernie was awarded the 2001 Max Born Award and is a Fellow of the American Physical Society, the Optical Society of America, and the American Association for the Advancement of Science. He is a member of the Biophysical Society. One of his hobbies is paleontology.

Yurke and his colleagues have created DNA “motors” – chemically operated devices 100,000 times smaller than the head of a pin. And in the growing field of nanotechnology, the manipulation of atoms and molecules, the idea of using DNA is viewed quite favorably. DNA stores huge amounts of information.

Nanotechnologists like Yurke and his team say that DNA is nature’s way of storing huge amounts of information in a tiny space. The space between each symbol in the genetic code is 0.34 nanometer (one billionth of a meter). Existing electronics technology makes features about 100 nanometers in size – more than 100 times bulkier than what DNA would provide.

Making a DNA-based computer would be another story. The DNA motors created by Yurke and his colleagues are so small that they don’t show up on optical microscopes. So the researchers must rely on fluorescence. Dye molecules are attached to the ends of the DNA strands and a laser is used to “excite” the dyes. Yurke says the closing and opening of the V-ends of the DNA motor (also called a “tweezer” because of its V shape) are measured by the amount of light being given off – noting that more light means the V-end is open, and less means it’s closed.

This interview was conducted by Haym Benaroya and took place between November and December 2001.

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Resonance: Nanoscience and technology are very exciting fields of research today. Also, major advances are being made in nanobiology with one goal being the utilization of nature’s building blocks for technological needs of people and society. Can you please summarize the essential aspects of your work, and then, what applications you have in mind that you are working toward?

Yurke: Information technologies have benefited tremendously by our ability to manufacture things on an ever-smaller scale. The continued shrinking of the transistor has made possible an exponential growth of computing power in personal computers, a trend that has lasted a quarter of a century. There is reason to believe that this trend will come to an end within a decade as the technologies used to manufacture these transistors are pushed to their limits. There is a search underway for alternative technologies that might allow one to go beyond these limits. This drives much of the current work in nanotechnology.

We now know that single molecules can serve as electronic switches. The challenge now is to figure out how to assemble such components together into complex information processing circuits. I am exploring the possibility of using molecules to direct the self-assembly of such circuits. DNA is a very convenient material to use in these investigations. Two strands of DNA will stick together to form a double helix only if their base sequences are complementary, that is, if each A of one strand matches a T from another strand and if each C from one strand matches a G from the other strand. If there are a sufficient number of base mismatches, two strands of DNA will not stick together. Thus, with sufficient care in picking base sequences, sets of DNA strands can be designed in which two DNA strands from the set will stick together only if their base sequences are complementary. Such sets of DNA are said to exhibit “molecular recognition.” By tagging molecular-scale electronic components with DNA strands, the DNA can direct the self-assembly of a complex network, in that, two components will be held next to each other only if they possess DNA strands whose base sequences are complementary. Such components when mixed together in a water solution will diffuse around and self-assemble into the network, the DNA acting as a kind of smart glue holding together those components that are supposed to be next to each other.

The construction of a DNA-based molecular motor was, for me, an exercise in learning how to do self-assembly using molecular recognition. Three strands of DNA were designed so that when mixed together in solution they would self-assemble into the V-shaped structures we refer to as molecular tweezers. The motor used to close and open the tweezers consisted of single strands of DNA extending from the arms of the tweezers. These single-stranded extensions could bind with complementary regions on a strand of DNA we called the fuel strand. By forming base pairs with these extensions, the fuel strand pulls the tweezers shut. The complement of the fuel strand is able to strip the fuel strand from the tweezers and restore it to its open configuration.

It is the self-assembly aspect of the DNA-based molecular motor research that is of most relevance to the assembly of molecular-scale electronic circuits using molecular recognition. However, knowing how to build molecular motors may come in useful for molecular-scale assembly as well. Whatever the assembly process, it will produce errors. Knowing how to build molecular motors opens up the possibility of devising molecular machines that could correct these errors.

Resonance: How far are researchers such as yourself from realizing your goals? Is this a realistic question?

Yurke: A wide variety of nanoscale structures have been fashioned out of DNA. Examples include wire frame polyhedra, tubes, sheets, and various kinds of molecular devices, such as our tweezers. Nadrian Seeman’s group at NYU did much of this work. The assembling together of nanometer-sized metallic wires using DNA has been demonstrated by Tom Mallouk’s group at Penn State. The assembly of a molecular-scale electronic circuit, using DNA-based molecular recognition, remains to be demonstrated, but I expect this to happen within a few years’ time. The big unknown is whether this type of assembly can be scaled up to assemble networks of sufficient complexity and with sufficient yield to be of interest to the electronics industry.

Closing of the DNA tweezers. The image shows the fuel strand (white ribbon) approaching the DNA tweezers. In the center image the fuel strand has made contact with the single-stranded extensions of the arms of the tweezers. As the fuel strand and the single-stranded extensions zip up to form double-stranded DNA the arms of the tweezers are pulled closed.

Resonance: One generally does not think of Bell Labs and Lucent as sites of bio-related research. Beyond the excitement and prestige of supporting such visionary research, where does Lucent see a payoff to its businesses from your research?

Yurke: Bell Labs has served the needs of two high technology companies, first AT&T and then Lucent. A part of this has been the development of tools for the characterization of materials and for the control of fabrication processes. The application of such tools to bio-related problems is one way of pushing their development. Much of the bio-related work that has been carried out at Bell Labs, including the application of nuclear magnetic resonance (NMR) to the investigation of biological problems and development of magnetic resonance imaging (MRI) technology, fits into this category. Bell Labs also serves as a source for new technologies relevant to the telecommunications industry. Biology sometimes provides inspiration for the invention of such technologies. Bell Labs researchers working in neurobiology, for example, devised neural network learning algorithms that have found application in adaptive software.

My foray into molecular biology was driven by the expectation that biology might have something useful to tell us about assembly at the molecular scale. For me, biology serves as a source of inspiration and as an existence proof that certain kinds of things can be done even though we may not yet know how to do them. One of the trends in electronic information processing technology has been the exponential decrease of component size. The recognition of this trend with its implication that in the not very distant future it may be useful to know how to assemble nanometer-sized parts into complex structures is one reason why my work has been supported.

Resonance: Are there many groups in the US working on DNA-based nanotechnology?

Yurke: The number of groups involved in DNA-based nanotechnology is small but growing. The ones that immediately come to the top of my mind are Nadrian Seeman’s group at NYU, Erik Winfree’s group at Caltech, Tom Mallouk’s group at Penn State, and Chad Mirkin’s group at Northwestern.

Resonance: What are the major stumbling blocks to progress? Size? Biochemistry?

Yurke: Currently the major hurdle is chemistry. Water soluble versions of molecules capable of electronic switching or of serving as molecular-sized electrical wires will have to be synthesized and new techniques will have to be devised for attaching these to DNA.

Resonance: In non-bio-nanotechnology, it is my understanding that one of the major challenges is to model across length and time scales. For example, if I want to build a rocket out of carbon nano-sheets, it would require that I understand the large-scale properties of the material as a function of the nano-scale properties. This knowledge would permit me to design the rocket structure properties more effectively. This is currently not possible. Is one of the goals of your research group to evolve DNA nanosystems so that they have large-scale applications? Then similar issues to those I described above would be a problem?

Yurke: Issues concerning how well self-assembly, using molecular recognition, will scale as the complexity of the structure being assembled increases will have to be addressed. Bulk materials properties are less of an issue in assembly since the assembled network is likely to be placed on a rigid support substrate or it may even be directly assembled on such a substrate.

Resonance: Speaking to a young person about 13-14 years old, just entering High School, what advice would you offer?

Yurke: My main advice is to learn as much as you can. If there is a particular profession that you would like to go into, try to find someone who works in that profession who can serve as a mentor. Get involved in activities relating to that profession. If you wish to go into a technical field, take as much science and math as you can. It will also help tremendously if you pick up a technical hobby that involves building things, conducting experiments, or making scientific observations.

Resonance: What are the great-unanswered questions in science today and in the forseeable future?

Yurke: I see several really big holes in our understanding of the physical universe. One is: “What is the universe made out of?” There is good evidence that 90% of the matter in the universe is not made of any substance that we are familiar with. This matter is referred to as dark matter because it is not directly observed through our telescopes. Its presence is inferred by the apparent existence of gravitational forces that cannot be accounted for by the matter we can see. Determining what this substance is will be a great challenge for cosmologists and particle physicists. The other really big hole in our understanding is: “How did life begin?” We have a very compelling theory for how life evolves but none of the suggestions for how it got started in the first place are compelling. Finding a compelling scenario for how the transition from nonliving to living took place presents a fascinating challenge.

Resonance: Why are so few scientists seen in positions of policy authority? Where is their education going “wrong”?

Yurke: My guess is that if one compares the fraction of the general population that are scientists with the fraction of positions in policy authority that are filled by scientists one will find that scientists are not underrepresented. However, with advances in medicine and technology and with the increasing stress the human population places on natural resources, scientific issues will be of increasing relevance in making policy decisions. So, scientists will have increasingly more to offer to this process. I think the scientific community owes a debt of gratitude to those who take time from their research to get involved in policy-making or in educating the public on scientific issues.

Resonance: You work with graduate students. Do you think that institutions of higher education are appropriately preparing this nation’s scientists for the future?

Yurke: I believe they are. It is to their own best interest that institutions of higher education insure that their students are competitive in the job market once they receive their degree. This makes them sensitive to the needs of society and industry.

Resonance: Where do we lose the scientific and mathematical interests of our junior and high school students? Especially women?

Yurke: I see this as more of a societal problem then as a problem with the educational system. I think the attitudes that parents hold toward education and towards the roles of women have a lot to do with this. I think this accounts for the underrepresentation of children from mainstream America, compared with first- generation immigrants and children of professional families, among those who go on to get advanced degrees. Among the reasons I would suggest for why mainstream America is relatively infertile ground for the production of scientists and other professionals are the following: It is still fairly easy to make a decent living without a higher education, so a good education is undervalued. Also, there is an undercurrent of anti-intellectualism in American society, some of which is a reaction to the challenges that scientific discoveries present to religious faith. Informing the public of the benefits it has received through science and communicating the adventure involved in scientific discovery may help in changing some of these attitudes.

Resonance: When did you realize that you wanted to study science and physics? Can you see yourself doing anything other than what you are doing at Lucent?

Yurke: I was always fascinated by the natural world. Already by the fourth grade I knew that I wanted to be a scientist. It was molecular biology that peaked my interest in physics. I was introduced to the world of molecular biology by a book I checked out from the children’s section of the Boise Public Library during the summer after I had finished the sixth grade. It described a world too small to be seen with an optical microscope, a world where DNA replication, protein synthesis, and the conversion of food into energy takes place. I wondered how it was possible to deduce what was going on in such a small world. So, the next time I visited the library I checked out a college textbook on molecular biology. The text was sprinkled with equations from physics and it had a large appendix on thermodynamics. I began to see the laws of physics as powerful tools for probing worlds beyond the direct reach of our ordinary senses and I also began to regard physics as foundational to all other sciences. From then on I was hooked on physics. Working at Bell Laboratories was the fulfillment of a childhood dream. I regard it a great privilege to work there. I have been given the opportunity to work in those fields in which I feel I can make the biggest contributions. There is no place where I would rather work.

Resonance: Can a degree in physics be viewed as a liberal education?

Yurke: A physics degree is a legitimate degree for a liberal arts institution to grant. But, receiving a liberal arts education implies that the education includes a healthy dose of the many types of intellectual endeavors that human beings engage in. The study of physics at the exclusion of coursework in the arts and humanities has too narrow a focus to count as a liberal education.

Resonance: What is an appropriate educational path for someone who wants to become a part of the nano-revolution?

Yurke: Most of the activity in nanotechnology is at the interface between physics, chemistry, and biology. I would recommend absorbing as much as one can of each of these fields. The focus in the physics education should be on condensed matter and its prerequisites: mechanics, electromagnetism, quantum mechanics, and statistical mechanics. Within chemistry the emphasis should be on physical chemistry and organic chemistry. Within biology the emphasis should be on molecular biology. Also, one should take a good laboratory course in electronics that covers instrumentation and measurement techniques.

Resonance: Is there a risk that corporations are relying too much on academic research? Isn’t this a long-term detriment to academic research, which really should be focused on research that has no obvious or immediate application? Isn’t this how many of our most important products evolved? For example, the output of Bell Labs in the 40’s-70’s?

Yurke: I think that it is fair that those who pay for the research have a major say in what research gets done. It is fair for a corporation to ask how the research it funds will contribute to its bottom line and it is fair for the taxpayer to ask how he or she will personally benefit by the research that his or her tax dollars go to support. It is up to us scientists to make our case for how we think research money should be spent so that those who pay for it will receive maximum benefit. Economic impact or the impact on public health should not be the only measures used to evaluate how research dollars should be spent. I believe that the discoveries of science have spiritual value and contribute to the enjoyment of life through the harmony and beauty they reveal. I think this is particularly true of space exploration and high-energy physics, where the medical and economic benefits are likely to be rather minor. But the case has to be made that what we are doing is worth the cost to those who are paying for it. The degree to which industry should rely on academic research and the mix of long-term and short-term research that should be present in academic institutions is also an issue that many parties have a say in and where scientists have to express their opinions of what is most appropriate.

Resonance: What are the roles of art in society? Does art do something for society that cannot be done by anything else?

Yurke: The ability to engage in rational thought is only a tiny aspect of what it means to be human. There are deeper aspects to human nature that make it possible for us to function as social beings. The arts are able to engage these deeper aspects and bring some of them to conscious examination. The arts allow us to explore, for example, what it means to live honorably. Such issues concerning moral judgment are of paramount importance in structuring a society but are beyond the realm of science to answer.

Resonance: How are art and science intertwined? Does science have a role in art?

Yurke: Both endeavors are searches for truth and beauty; and much of art and science springs from a common human urge: the desire to understand the universe and one’s place within it. Science really is a form of art. It is a creative activity of the mind that would be impossible without an imagination. Mathematical symbols are the brush strokes we use to paint our portraits of the universe. The aesthetic qualities we look for in our artwork are simplicity and detail. We are minimalists employing Occam’s razor. We strive to capture the entire universe in a single equation. We are also realists, awed by precision agreement between theory and experiment. Our craft has magic qualities, including an uncanny predictive power.

Science and art both have the power to transform the world. The Copernican revolution, the industrial revolution, Darwinian evolution, and modern physics have all greatly influenced how we view ourselves, and this has had a significant effect on the art world. The images produced by science, such as the earth rising over a cratered moonscape, and the products of science, such as machinery, rockets, and nuclear weapons, provide artists with provocative symbols of the human spirit and of good and evil. Artists are technicians, skilled at operating their instruments, and they often quickly adopt new technologies when these will help in their craft. The fruits of science, such as photography, radio, movies, television, computers, and the Internet, have provided new media for artistic expression and have given rise to new art forms. Science, through what it has revealed about the universe and especially through the technology it has spawned, has had a tremendous effect on art.

Resonance: And what about the role of art in science?

Yurke: For the scientist, art serves as a source of inspiration, occasionally as a source of metaphor for scientific activity, and sometimes as a conscience reminding us of our social responsibilities. But, I think, art has had considerably less influence on the practice of science than science has had on the practice of art. Given the diversity of beliefs, cultural practices, and artistic styles that distinguish various cultures, science exhibits a surprising uniformity that transcends cultural boundaries and time. Sure, there is bickering as we sort things out at the edge of the unknown, but these are small ripples on a deep sea of consensus. Why is there this uniformity in this cultural activity we call science? We are listening to Mother Nature and we all hear her sing the same song.

Resonance: Where are the greatest challenges today to American society? Are you optimistic with the trends?

Yurke: The great challenge confronting American society is to remain American. We have created a society where the individual has been greatly empowered, and, although there is always room for improvement, it has done well in dealing with diversity. It is a society that recognizes the value of a limited government and of the need to protect the rights of the individual. It recognizes the importance of the right to voice one’s opinions. It also recognizes that religion is a personal matter dictated by one’s own conscience, a matter that government should be neutral towards. It is my hope that American society will be able to resist the pressures of special interests and the temptations that arise during times of national crises or during economically hard times to back-pedal on some of these ideals. At the present the trends appear mixed to me.

Resonance: If you could solve just one of humanity’s problems, which one would it be?

Yurke: Much of the world is currently enjoying a level of prosperity that is unprecedented in human history. When I think about the long term, however, an earth depleted of its resources comes to mind and I wonder if a poor, starving, diseased, and overcrowded mass of humanity in a dusty, sun-baked world is mankind’s ultimate destiny. I wish I could do something to insure the long-term prosperity of humanity.