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Using DNA to Search for Dark Matter

by John G. Cramer

Alternate View Column AV-91
Keywords: dark matter WIMPs weakly interacting massive particles detection DNA eV energy deposition
Published in the September-1998 issue of Analog Science Fiction & Fact Magazine;
This column was written and submitted 02/20/98 and is copyrighted ©1998 by John G. Cramer.
All rights reserved. No part may be reproduced in any form without
the explicit permission of the author.

     Physics research has a long and successful track record of using new tools taken from evolving technologies to investigate important physics issues. In this column, I want to describe a new and novel proposal for detecting dark matter using a new technology which, up to now, has never been employed in cutting-edge physics experiments: the new technology of molecular biology that has recently been developed for the Human Genome Project. In particular, I will discuss a proposal for detecting WIMPs using DNA molecules. Let us start with a discussion of WIMPs and the Dark Matter Problem.

    Over the past two decades we have come to realize that the ordinary matter of our universe, the stuff that forms quasars, galaxies, stars, planets, people, atoms, quarks, ..., is only an insignificant fluff, a minor impurity that permeates the real material of the universe, the unknown invisible substance called "dark matter" [See my previous Alternate View column "The Dark Side of the Force of Gravity", Analog, February-1985]. Dark matter accounts for more than 90% of the total mass of the universe, yet we have no idea what it is.

    Astronomers discovered dark matter while using the Doppler-shift technique to measure the velocities of bright stars orbiting distant galaxies and galactic clusters. Roughly speaking, any orbiting object must have a velocity that depends on the square root of the amount of mass within the spherical volume enclosed by its orbit. As the distance R of the bright star from the center of the galaxy or cluster increases, it is expected that the star's orbital velocity should first increase in proportion to R, as long as it is at a radius within which the stars of the galaxy are distributed fairly uniformly. When the bright star is at a large radius outside the galaxy, so that the sphere of radius R encloses essentially all of the mass of the galaxy or cluster, the velocity of the star should fall off as the inverse square root of R. Thus, the average mass and mass distribution of a galaxy can be estimated by measuring the velocities of a number of bright stars at various distances from the galactic center.

    To the surprise of astronomers, the velocities measured in this way were much larger than expected from a galactic star count, and it was found that the orbital velocity continued to increase with R far beyond the visible radius of the galaxy. This is convincing evidence that the visible mass of a galaxy, even after correcting for non-luminous "brown-dwarf" stars and interstellar gas, is much too small and too localized to account for the observed orbits. The conclusion from this work is that most of the mass of galaxies comes from some mysterious dark matter. Furthermore, this invisible dark-matter mass is distributed much more broadly than the visible stars in the galaxies studied. This mystery of the origin of this extra mass has come to be known as "The Dark Matter Problem". It is one of the outstanding unsolved problems of contemporary astrophysics.

    The Dark Matter Problem has prompted a close examination of all theoretical possibilities for the missing mass of the universe. Theoretical particle physicists over the years have predicted scores of could-be particles that have never been observed in the laboratory, and many of these have become "dark-matter candidates", particles which, if they existed, might account for the hidden mass of the universe. Among these dark matter candidates are axions [see my February-1985 Alternate View column in Analog], massive neutrinos [see my September-1992 column], and more generally, a whole class of weakly interacting massive particles otherwise known as "WIMPs" [see my May-1986 column]. Many experimental physics groups have initiated searches targeted on one or more of these candidate particles, but none have been successful. There have been some inconclusive hints of neutrino mass effects, of larger-than expected brown dwarf contributions to galactic mass, and perhaps of a non-zero cosmological constant that might give space itself a significant mass density. However, at this writing (2/98), no "smoking gun" has been found to reveal the secret identity of dark matter particles.

    In a typical neutrino or WIMP search, a large dense volume of sensitive detector material is placed underground in a low- radiation environment. Examples of such experiments are the solar neutrino detectors (e.g., Homestake, Kamiokande, SAGE, SNO, etc.) placed deep underground in a mine, with the mine location selected so that background from radioactive decays in the surrounding rock is low and so that the detector is deep enough underground to be well shielded from cosmic rays, particular the highly penetrating mu mesons. The detector material is chosen so that interaction with the particles of interest, e.g., dark matter WIMPs, produce detectable change in detector material or directly generate a detectable signal.

    For example, an energetic neutrino may be detected by transmuting detector material into a radioactive isotope (as in the Homestake 37Cl based neutrino detector) or by producing a flash of light arising from scattering, interactions, ionization, and Cerenkov radiation (as in the SNO and Kamiokande detectors). In either case, for each detected particle a large amount of energy must be deposited to produce the transmutation or ionization that constitutes the signal. Transmutation requires deposition of 2 to 10 million electron volts of energy, while production of Cerenkov light flashes from ionization in water requires an energy deposition of 1 million electron volts or more. However, adding scintillation chemicals to the water can reduce the minimum energy to around 100 electron volts. If less energy than this is deposited, the detector will not produce a signal. (Note: to set the scale, 2 electron volts is roughly the energy content of one photon of visible yellow- orange light, and 511,000 electron volts is the mass-energy of one electron.)

    Dark matter has not so far been detected by existing experiments, and perhaps this is not surprising. Theoretical calculations suggest that interactions of matter with WIMPs may liberate only a few electron volts of energy. Therefore, to "push the envelope" of dark matter searches physicists must design a new generation of detectors that can function with a smaller deposition of energy per detection event. This might be accomplished, for example, with a small gas- filled detector or with a phonon-sensing solid state device. However, such detectors are too small and/or too low in density for efficient detection, and one might have to wait many centuries to detect enough events for a believable signal. It is much more difficult to design the sensitive large- volume high-density detectors needed for efficient WIMP detection.

    Dr. Richard J Muirhead and his collaborators at the University of Washington have proposed an innovative solution to this problem. It exploits the properties of the molecules of life, DNA. The amount of energy required to break a single chain of DNA is on the order of 10 electron volts, at least a factor of 10 lower than the energy threshold of previous detectors. The Muirhead scheme suggests placing a large volume of DNA solution in a well-shielded location and monitoring the rate at which DNA chains are broken.

    Single DNA chains with a repeating single purine base, for example an adenine chain of the form A-A-A-..., are commercially available in bulk quantities and in a variety of lengths. Using standard molecular biology techniques, a molecule of biotin (C10H16N2O3S, a colorless crystalline member of the vitamin B complex) is attached to one end of a 20-base DNA chain, and a fluorescent probe molecule (FITC) is attached to the other end.

    A large quantity of these molecules are placed in a water solution and exposed to WIMPs or to calibrated amounts of radiation. After a suitable exposure, the solution is passed through a streptavidin column. Streptavidin has a remarkable affinity for biotin and binds to it with a very high probability, so that the biotin ends of all the DNA chains should be captured in the streptavidin column, but any fluorescent FITC end of a broken DNA chain will flow through the streptavidin column without interaction. The solution from the column is then exposed to ultraviolet light and its fluorescence accurately measured, thereby providing a quantitative indication of the number of DNA chains broken during the exposure.

    A more sensitive variation of the same technique, currently under consideration, might attach a strand of RNA rather than FTIC to the DNA ends, and then use an RNA amplification technique similar to the polymerase chain reaction (PCR) to repeatedly duplicate any RNA from broken chains. This might permit the detection of one single broken DNA chain which occurred during the exposure, out of all of the DNA in a large volume of solution.

    This scheme for searching for WIMPs is still in the development and proposal stage, has not yet received major funding, and has not been tried on a large scale, but it offers the promise of bringing greatly increased sensitivity to investigations of the Dark Matter problem. However, even before this type of WIMP search has been attempted, there is some circumstantial evidence that it may be on the right track, evidence again supplied by the biological sciences.

    The Earth orbits the Sun with an orbital speed of about 29,800 meters per second, about 0.01% of the velocity of light. If the WIMPs orbiting the center of the galaxy are in our vicinity, we should encounter more of them when the Earth's orbital speed is directed against the WIMP stream then when it is directed with the stream. Therefore, if WIMPs break DNA chains, one might expect a yearly variation in the mutation rates of living organisms. Two groups have looked for annual variations in the mutations rate of fruit flies, an insect widely used in laboratory-based mutation experiments. Both groups found that there is about a 15% variation in the mutation rate over the course of a year. These results are not conclusive, since such annual variations might have other causes (variations in environmental light intensity, humidity, temperature, etc.), but they suggest that there could be some validity to the notion that WIMPs can break DNA chains.

    Will the Dark Matter problem be solved using DNA and the techniques developed for the Human Genome Project? That is difficult to say. The method described above has the needed sensitivity to small energy deposition, but there are very formidable problems with background that must be addressed and overcome before it can be used for quantitative measurements. And the method has the disadvantage that one must essentially destroy the detector in order to read out a signal, removing all of the detector's DNA to the streptavidin column in order to make a measurement. Some flow- through scheme would be preferable, in which broken chains were continuously removed from the solution, but the unbroken DNA chains were returned to the solution and remained as active detector elements. But in any case, this technique represents a new synthesis which brings ideas from both physics and molecular biology to a sharp focus on an important fundamental problem, the basic structure of the universe. This is perhaps the first example of a brand new trend in basic physics research.

John G. Cramer's 2016 nonfiction book (Amazon gives it 5 stars) describing his transactional interpretation of quantum mechanics, The Quantum Handshake - Entanglement, Nonlocality, and Transactions, (Springer, January-2016) is available online as a hardcover or eBook at: or

SF Novels by John Cramer: Printed editions of John's hard SF novels Twistor and Einstein's Bridge are available from Amazon at and His new novel, Fermi's Question may be coming soon.

Alternate View Columns Online: Electronic reprints of 212 or more "The Alternate View" columns by John G. Cramer published in Analog between 1984 and the present are currently available online at: .


Interactions of WIMPs with matter:
P. F. Smith and J. D. Lewin, Physics Reports 187(5), 203-280 (1990).
Detecting WIMPs with DNA:
R. Muirhead, R. Puff, and J. Lord, Bull. Am. Phys. Soc. 42(7), 1680 (1997).

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