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Overall, however, the implication is that thetiming of many recent events in human evolu-tion has been overestimated by past studies.Examples include the divergence betweenhumans and Neanderthals — new estimate354,000 years ago (range 222,000 to 705,000years ago, against a current range of 317,000 to853,000 years ago); and the last split withinthose Neanderthals that have been sequenced— 108,000 years ago (range 70,000 to 156,000years ago compared with a current range of151,000 to 352,000 years ago).

Second, can the acceleration be explained?One approach is as follows. We can subdividethe deleterious mutations into the proportionsthat are very slightly deleterious, ��, slightlydeleterious, ��, and deleterious (but not lethal),���. Deleterious mutations are not expected tobecome fixed in large populations, but never-theless can persist in the population for longperiods of time. The average time before loss(see ref. 7, for example) correlates with deleteri-ousness, so persistence time increases from ���

to �0. Thus, as observation times diminish, weshould observe a greater proportion of slightlydeleterious mutations that have yet to be lost,with the most deleterious (���) observed onlyin the short-term pedigree studies. This givesthe apparent acceleration in mutation rate asthe separation times between sequencesdecrease. A qualitative explanation such as thisis straightforward, but the effect requires quan-titative treatment and thorough testing.

Third, why wasn’t the short-term accelera-tion picked up earlier? There were hints.Kimura1 (page 45ff.) comments that his calcu-lations assumed sufficient time for loss or fix-ation of a neutral mutant, and that at shorterintervals there would be higher variability.Some of the increase in rate comes fromneutral mutations (Fig. 1a), and some fromslightly deleterious mutations. In early molec-ular work, the genetic diversity within pop-ulations — heterozygosity — was measured bythe differences in the behaviour of variant pro-teins in electrophoresis, and long-term evolu-tion by differences in amino-acid sequencesbetween species (with only one sequence stud-ied per species). Thus, direct comparabilitywas not possible in those early studies —although in 1977 Ohta did point out8 that “Inthe future, it is likely that genetic variabilitywill be detected at the level of amino acid ornucleotide sequences”.

For some reason, the continuum betweenpopulation heterozygosity and long-termevolution has not been adequately studied.Although it is a continuum, the techniquesrequired may change as the timescaledecreases. For example, some concepts fromlong-term evolution (binary evolutionarytrees with sequences studied only at the tips)have been extended into populations wheretrees are no longer binary, and ancestralsequences (at internal nodes) are still presentin the population. There are hints that a formalmultiscale study9 is necessary, because even

though the same underlying process is occur-ring, different features of trees are observed asthe timescale changes (Fig. 1b, c).

Finally, what are the consequences of Hoand colleagues’ conclusion5? As they point out,the obvious ones are practical, in that manytime estimates require recalculation — includ-ing the times of events in recent human evolu-tion (such as origin of the Polynesian geneticmarker that distinguishes Polynesians from allother human populations10), and the origin ofRNA viruses such as HIV11. In some cases theconstraints are from recent events, and it is thelong-term events that require re-analysis.

Much more remains to be done. There is thechallenge of formulating a single theory thatoperates smoothly over disparate timescales,from current heterozygosity to the long-termrate of evolution. In addition, a single muta-tion rate (�) does not really exist. Even fornucleotides there are many ‘mutation rates’, atleast one between each pair of nucleotides, andthese can be estimated separately using three-

dimensional matrices12. The J-shaped curvecannot rest until a single theory holds for it: welive in interesting times. ■

David Penny is at the Allan Wilson Center forMolecular Ecology and Evolution, MasseyUniversity, Private Bag 11222, Palmerston North,New Zealand.e-mail: D.Penny@massey.ac.nz

1. Kimura, M. The Neutral Theory of Molecular Evolution(Cambridge Univ. Press, 1983).

2. Garcia-Moreno, J. J. Avian Biol. 35, 465–468 (2004).3. Howell, N. et al. Am. J. Hum. Genet. 72, 659–670 (2003).4. Lambert, D. M. et al. Science 295, 2270–2273 (2002).5. Ho, S., Phillips, M. J., Cooper, A. & Drummond, A. J. Mol.

Biol. Evol. 22, 1561–1568 (2005).6. Dickerson, R. E. J. Mol. Evol. 1, 26–45 (1971).7. Garcia-Dorado, A., Caballero, A. & Crow, J. F. Evolution 57,

2644–2646 (2003).8. Ohta, T. Theor. Popul. Biol. 10, 254–275 (1976).9. Penny, D. & Holmes, S. Trends Ecol. Evol. 16, 275–276

(2001).10. Oppenheimer, S. J. & Richards, M. Nature 410, 166–167

(2001).11. Rambaut, Q., Posada, D., Crandall, K. A. & Holmes, E. C.

Nature Rev. Genet. 5, 52–61 (2005).12. Ota, R. & Penny, D. J. Mol. Evol. 57, S233–S240 (2003).

CANCER BIOLOGY

Sleeping Beauty awakensKeith C. Weiser and Monica J. Justice

Ancient jumping DNA found napping in fish has been revived and is beingused to identify cancer genes in mice. But the benefits of this aptly named‘Sleeping Beauty’ system could reach far beyond cancer.

Transposable elements are discrete pieces ofDNA that can jump around in the genome of aliving organism. These elements were initiallydiscovered in corn through the Nobel-prize-winning work of Barbara McClintock1, andthey have been found in organisms through-out the tree of life. For each DNA transposon,a corresponding protein, called a transposase,mediates the jumping. One such transpo-son/transposase duo, aptly named SleepingBeauty (SB), was found latent in the genome ofsalmonid fish. Its DNA sequence had mutatedto the point where it no longer jumped, butrather slumbered as inactive ‘junk DNA’. Theextinct SB jumping functions have been resur-rected2, and in this issue Dupuy et al. (page221)3 and Collier et al. (page 272)4 presentimprovements to this technology and exploitthe system to identify genes involved in cancer.

Many agents, including chemicals, radiationand viruses, are routinely used to disrupt genesrandomly, with the aim of identifying genefunctions and the diseases associated withthem. But it can be extremely difficult to findwhere a random mutation has been intro-duced, requiring huge amounts of sequencingto pinpoint each tiny change. Transposableelements are powerful reagents in this regardbecause their sequence is known, so when theymutate genes they provide a ‘tag’ that pin-

points their location in the vast sea of genomicDNA. Tagging genes by insertion is not a new idea, and geneticists working on manyorganisms use transposable elements. Theyhave been little used in mice, however, becauseknown transposons hop around the mousegenome very infrequently, yielding few newmutations.

The two groups surmounted this problemin two ways. Collier et al.4 engineered an SBtransposon (T2/Onc) to have the ability toenhance or disrupt genes. They used this in astrain of mice that produce the SB transposase in all their cells and which have mutations that make them especially susceptible tocancer (Fig. 1). Dupuy et al.3 redesigned thetransposon to be smaller (T2/Onc2), andcreated a mouse strain whose cells containedincreased amounts of transposase, leading tohigher mutation rates. A major advantage ofthe SB system over viral or previously usedtransposon systems is that, because the trans-poson comes from fish, it is distinct from thelarge number of native transposons present5,making it easy to find the exact site(s) in thegenome where SB integrates.

The authors used their system to search forgenes that cause cancer, as genes identified in mouse cancer are often also perturbed inhuman cancer. To understand how SB can

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50 YEARS AGOAnother milestone was reachedin the history of the EuropeanOrganization for NuclearResearch, when on June 10 the foundation-stone was laid of the laboratories at the Meyrinheadquarters of the Organizationnear Geneva, followed by thesignature of an importantAgreement between theOrganization and the SwissGovernment… Those who have been closely associatedwith the years of planning cameaway feeling that this uniqueOrganization has good reason to be proud of what has beenachieved so far. The high level of scientific and technicalcompetence of the research anddesign teams and the spirit ofenthusiasm which animates allconcerned provide solid groundsfor confidence in the healthygrowth of the new Organization.From Nature 16 July 1955.

100 YEARS AGO“The popularisation of science.”The New Knowledge by RobertKennedy Duncan. The author of this attempt tomake the progress of recentdiscovery in chemistry andphysics understanded of thepeople remarks in his preface:—“The great expositors are dead,Huxley and Tyndall and all theothers; and the great expositor of the future, the interpreter ofknowledge to the people, has yet to be born.” And (but it mustbe added quite modestly) heattempts to wear the cloak ofprophet… To give the reader an idea of the author’s style, a quotation from the firstparagraphs of part ii may bemade… “Here, for example, is a swarm of atoms, vibrating,scintillant, martial,— they call it a soldier,— and, anon, somethousands of miles away uponthe South African veldt, thatswarm dissolves,— dissolves,forsooth, because of anotherlittle swarm,— they call it lead.”…Now this purports to be very finewriting, but does it gild the pill ofscience? I am inclined to thinknot. Still, tastes may differ.From Nature 13 July 1905. 50

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identify cancer genes, imagine the genome asa book of instructions on how cells work. SB islike a small phrase or set of directions that canhop into, and potentially alter, any instructionin the book. Sometimes, inserting the phrasewill cause insignificant changes, but if SB altersinstructions for key processes, such as cellproliferation or cell death, the cells can growand divide beyond their normal potential andbecome cancerous. The authors designed theSB transposon to disrupt gene function in two ways. If it inserts in a gene, it will truncate the protein encoded by that gene, usuallydestroying its function. This will identify genesthat help to protect against cancer (tumour-suppressor genes). If the transposon insertsnear a gene, it causes an increase in the geneproduct, allowing cancer-promoting genes(oncogenes) to be identified.

By isolating the sites of SB insertion intumours, the groups tagged genes that areknown to be important in the development ofcancer and those likely to be involved in thedisease that had not previously been associ-ated with it. Dupuy et al.3 also demonstratednetworks of genes that interact to cause cancer.In addition, Collier et al.4 show, using animalsthat harbour cancer-predisposing mutations,that the SB system can tag genes in a solidtumour called a sarcoma. This tumour caninvolve various tissue types, including neuralcells and connective tissue cells.

Cancer is rarely caused by the mutation of a

single gene; rather, perturbations of severalgenes tend to cooperate to cause the disease6.Genetic pathways involved in the develop-ment of leukaemia have been dissected by tagging with mouse leukaemia retroviruses7,8,but gene networks in other tumour types areless well studied. The development of newtreatment strategies would ideally requireinformation on all the genes involved in com-mon and devastating cancers such as breast,colon, prostate and lung cancer, and the SBsystem seems a promising way to provide this.

The technology is likely to be very powerful,because the transposase can be designed to beexpressed selectively in a specific cell type ordevelopmental stage, so that transposition willoccur only in those cells or at that time. Manycancer-associated genes are disrupted in onlyone particular cancer, and the selective SBtechnique can be used to locate these. Further-more, the ability to limit transposase expres-sion will enable the system to be turned on tomake mutations and then turned off to stabi-lize them. It also allows for the controlled exci-sion of the transposons, so that mutations canbe reversed.

At present, however, the ability to restrictgene expression to each type of tissue-specificstem cell is limited9. (Tissue-specific stem cells are the immature cells that give rise to specialized tissues, where cancer mutationsare most likely to occur.) Further research into stem-cell-restricted gene expression

Figure 1 | DNA leaps out of fish and into cancer research. a, Mice whose cells contain many copies ofthe Sleeping Beauty transposon from fish are bred with mice whose cells make the SB transposase athigh levels. Cells in the offspring contain both the transposon and transposase (pacman), allowing thetransposon to hop about the genome. b, The transposase binds to and excises the transposon from itsstarting location in the genome. The excised transposon can reintegrate elsewhere in the genome,sometimes near to or within a cancer-related gene. If the transposon inserts in a gene, it will truncatethe encoded protein, usually destroying its function. This will identify genes that help to protect againstcancer (tumour-suppressor genes). Inserting near a gene causes an increase in gene product. This willidentify cancer-promoting genes (oncogenes).

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theory of quantum chromodynamics (QCD).Without this strong force, which not onlybinds quarks to form protons, but also keepsprotons together in the nucleus, matter wouldsimply fall apart.

The fundamental particles possess a widerange of masses: an electron is about 360,000times lighter than the heaviest, or ‘top’, quark.In the standard model, the origin of the mass of fundamental particles is the yet-to-be-discovered Higgs force field. The reasonelectrons and quarks have the exact massesthat they do must, however, come from adeeper theory of nature. Physicists hope thatgaining knowledge of the quark masses willguide them to that theory.

As quarks are permanently bound intocomposite particles (Fig. 1), it is not possible to determine their masses directly. Theoristsinstead solve the equations of QCD for a com-posite particle made up of quarks (protons andneutrons are examples) with the quark massesand strength of the strong force as unknowns.The most likely value of a quark mass is thatwhich best reproduces the measured mass ofthe composite particle. As energy is related tomass through E�mc2, where m is the mass ofthe particle and c the speed of light, this massdepends not only on the mass of the con-stituent quarks, but also on the bonds betweenthem (potential energy) and their motion(kinetic energy).

The mass of a hydrogen atom is less than themass of its constituents by the electromagneticbinding energy (�13.6 electronvolts) — aneffect of 1 part in 100 million. The effect of thestrong force is greater: the mass of a nitrogennucleus, with seven protons and seven neu-trons, is less than the mass of its constituentsby a binding energy of �105 megaelectron-volts (MeV), 0.7% of the total mass. This is the formidable energy that is released in nuclearfission and fusion reactions.

The binding effects between quarks are fun-damentally different from those in atoms and

PARTICLE PHYSICS

Weighty questionsIan Shipsey

In an unprecedented feat of computation, particle theorists made the mostprecise prediction yet of the mass of the ‘charm–bottom’ particle. Dayslater, experimentalists dramatically confirmed that prediction.

The lofty endeavour of particle physicists — tounderstand the birth, evolution and ultimatefate of the Universe by studying its fundamen-tal particles — has just received a significantboost. The fiendishly difficult equations of thestrong nuclear force have yielded to a 30-yeareffort to allow the first precise prediction of a composite particle’s mass1, a predictionpromptly confirmed by experiment2. Thecomputational technique responsible, latticequantum chromodynamics, could also beused to estimate quark masses better, to shedlight on the origin of mass, and to reveal howthe Universe, originally made of matter and

Figure 1 | Gregarious quarks. a, Free quarks do not exist. In a proton, for example, the three principal quarks — two ‘up’ (u) and one ‘down’ (d) — are boundwith a force of more than 10 tonnes by the exchange of gluons (curly lines). Additional gluons and quark pairs are constantly emitted, only to be reabsorbed;just a fraction of this swarm of particles is shown here, and for clarity the gluons that pass between the d quark and u quark in the proton are not shown. b, Tug on one of the three quarks in a proton, and c, by the time the separation is a proton radius (about 10�15 m), enough work has been done to produce a quark and an antiquark. d, The antiquark latches on to the quark to form a quark–antiquark state called a �-meson; the new quark replaces the original in the proton. The ‘charm–bottom’ particle, the mass of which was predicted by Allison et al.1, is a heavier variant of the �-meson, containing a ‘charm’ quarkand a ‘bottom’ antiquark.

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will expand the application of the SB system. The SB system of genome manipulation and

mutation will be valuable in organisms otherthan mice, and has applications outside cancer.It can be used in human cells, or in any organ-ism that is a model for human disease. Thetransposon can be engineered to deliver anyDNA cargo to many locations in the genome.This has remarkable potential for discoveringthe genes associated with diseases that have agenetic component (heart disease, diabetes,birth defects, and many more). It might alsoprovide therapeutic gene delivery and large-scale genome modification. With the genomesequences for many organisms nearly com-plete, the utility of this beautiful tag for DNAmutations is infinite. ■

Keith C. Weiser and Monica J. Justice are in theDepartment of Molecular and Human Genetics,Baylor College of Medicine, One Baylor PlazaS413, Houston, Texas 77030, USA.e-mail: mjustice@bcm.tmc.edu

1. McClintock, B. Proc. Natl Acad. Sci. USA 36, 344–355(1950).

2. Ivics, Z., Hackett, P. B., Plasterk, R. H. & Izsvak, Z. Cell 91,501–510 (1997).

3. Dupuy, A. J., Akagi, K., Largaespada, D. A., Copeland, N. G.& Jenkins, N. A. Nature 436, 221–226 (2005).

4. Collier, L. S., Carlson, C. M., Ravimohan, S., Dupuy, A. J. &Largaespada, D. A. Nature 436, 272–276 (2005).

5. Brosius, J. Bioinformatics 19 (Suppl. 2), ii35 (2003).6. Vogelstein, B. & Kinzler, K. W. Trends Genet. 9, 138–141

(1993).7. Suzuki, T. et al. Nature Genet. 32, 166–174 (2002).8. Hansen, G. M., Skapura, D. & Justice, M. J. Genome Res. 10,

237–243 (2000).9. Marx, J. Science 301, 1308–1310 (2003).

antimatter in equal proportions, ended upcontaining just matter.

The ‘standard model’ of particle physicsdescribes the interaction of fundamental par-ticles, such as quarks and electrons, as theexchange of other particles that convey force.In an atom, for example, electrons bind to protons by swapping massless photons — thefamiliar electromagnetic force encompassedby the theory of quantum electrodynamics(QED). Similarly, inside the proton, ‘up’ and‘down’ quarks bind by exchanging masslessparticles called gluons — an interactiondescribed by the so-called strong force and the

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