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Vol 446|15 March 2007

BOOKS & ARTS


Biological programming
The digital nature of molecules such as DNA means they can be used in computers.

some sobriety into the narrative,

A. PASIEKA/SPL
Genesis Machines: The New Science of lest the reader believes that home
Biocomputing computers running on DNA are
by Martyn Amos
just around the corner. Indeed, he
Atlantic Books: 2006. 320 pp. £18.99
points out right from the begin-
Christoph Adami ning that DNA computation is
When visiting the Santa Fe Institute in autumn unlikely to replace its silicon-based
1994, I was chatting with Chris Langton when forerunner, but rather be confined
Stuart Kauffman came running down the hall to special problems. What these
waving a manuscript and shouting unprinta- will be is not at all clear, because
bles. When we cornered him, he was slapping the initial excitement about DNA’s
his forehead mumbling: “I could have done ability to tackle problems in the
this, if I had only thought of it!” It turns out most difficult category, such as
that ‘this’ was the first example of a DNA-based factoring a number into its prime
computation, carried out by Leonard Adle- components, quickly waned when
man of the University of Southern California, it became clear that thousands of
launching the field of DNA computation (Sci- litres of DNA would be necessary
ence 266, 1021–1024; 1994). Martyn Amos’s to solve problems that are now just
book Genesis Machines looks back on the 12 beyond the reach of conventional
years since this event, and speculates about the computers. But Amos insists that
future of the increasingly intertwined fields of DNA computation is interesting
biology and computer science. in its own right because of the
The computational feat reported in Adle- lessons it teaches us about com-
man’s seminal article was innocuous enough: putation in biology. The last two
examine a graph of seven nodes, and determine chapters are therefore devoted to
whether a one-way path exists that connects all endeavours only indirectly related
the nodes once and only once (an example of to the quest for a DNA-based com-
the hamiltonian path problem). But the impor- puter, namely DNA self-assembly
tance of this work did not lie in the sophisti- and synthetic biology.
cation of the problem, but in the fact that it As Amos explains, the stabil-
showed that strands of DNA, mixed together in ity of DNA and its digital nature
a vial, could be controlled such that their bio- can be used to create — or should
chemistry could be viewed as a computation. we say program — structures on
And this is perhaps the central message that a nanometre scale, a feat that is
Amos tries to convey in his book: all physical Programmable computers have been developed that use DNA. exceedingly difficult to achieve
systems can be viewed as performing computa- using non-biological material.
tions; it is down to the skill of the investigator Perhaps one of the weaknesses of this book Inspired by the pioneering work of crystallo-
to make them perform useful ones. is a result of the unavoidable interdiscipli- grapher Ned Seeman at New York University,
Since 1994, DNA computation has advanced nary nature of its subject. For the lay reader Erik Winfree and Paul Rothemund of the Cali-
considerably, and programmable computers for whom this book is written, the concepts of fornia Institute of Technology set out to show
have been developed using DNA molecules Turing universality, the complexity of ‘P versus that DNA can be programmed to fold into arbi-
only and with no moving parts. But for the NP’, and the biochemistry of DNA are likely to trary structures whose intricacy can only be
reader to appreciate the story of how vials of be difficult subjects, and Amos’s introductions revealed by atomic force microscopy.
DNA molecules could be coaxed to do some- include biographical sketches of their main Synthetic biology, on the other hand, con-
thing nature never intended, Amos has to protagonists. As a result, more than 100 pages cerns the creation of biological systems from
reach far beyond the basic biochemistry of go by before Adleman’s pioneering experi- scratch or from components that had other
DNA, to the origins of computer science and ment can be described in detail, and even then functions. Behind it lies the concept that we
complexity theory. Indeed, DNA computa- it is interrupted by a narrative of the trials, do not need to understand every single detail
tion was not the brainchild of biologists, but tribulations and ultimately triumph of Kary of a complex system in order to be satisfied
computer scientists who became fascinated Mullis and his discovery of the polymerase with what we know. After all, very few people
by the ‘digital’ nature of DNA and its role in chain reaction. understand down to the level of the electron-
information processing. The roots go back to Nevertheless, the central discoveries in this ics the workings of my laptop computer. But
luminaries such as John von Neumann and rapidly evolving field are covered, and the this does not worry me because I know that
Alan Turing, and Amos goes to considerable inevitable critics of this endeavour are not someone knows how to make it, so there is suf-
lengths to expose these foundations. overlooked. Amos does a good job of injecting ficient knowledge to create another one just
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BOOKS & ARTS NATURE|Vol 446|15 March 2007

like it. The same can be said for biomolecular studies the many ways in which organisms orders are unknown, so it would be impossible
systems: we may never be able to comprehend can actively restructure their genetic material, to restrict the contents of chapters to strictly
every molecular interaction within a cell, but if believes that such processes should be more monophyletic units. Nowadays, taxonomists
we can build a system that behaves just like its widely incorporated into evolutionary think- have to deal with two different taxonomies: a
natural counterpart, then perhaps we should ing. Although Darwin could not possibly have traditional one, based on morphology, and a
be satisfied with that. anticipated such processes, they follow the modern one, based on molecular analysis. Each
Amos’s account of the different paths to general darwinian paradigm and do not, in my chapter begins with an introduction describing
synthetic biology covers most of the recent opinion, necessitate a ‘third way’ somewhere our changing views on the relationships of the
advances that have made the headlines. These between creationism and what Shapiro calls animals to be discussed. These introductions
range from pieces of DNA called ‘biobricks’ ‘neo-darwinian orthodoxy’. show the perspective and knowledge that Rose
and the ‘repressilator’ to a way of coaxing yeast But apart from this quibble, this is an enjoy- uses when examining the data. When avail-
to produce the precursor for a malaria drug able book that could perhaps have profited able, he provides two alternative cladograms
— a feat for which Jay Keasling, a biochemical from more illustrations to convey some of the showing the relationships among the studied
engineer at the University of California, Berke- computational and experimental methods. forms, one based on morphology, the other on
ley, won Discover magazine’s first ‘scientist of I recommend it to anyone interested in com- molecular studies. His preference is decidedly
the year’ award. putation writ large who is not afraid to cross morphological, as is evident from his attitude
But I have to take Amos to task for present- disciplinary boundaries that once seemed to the clade Afrotheria.
ing the work of James Shapiro, a microbiologist impassable. ■ The notion of Afrotheria arose around 1990,
at the University of Chicago, as if his investiga- Christoph Adami is at the Keck Graduate based on DNA analyses demonstrating that six
tions of the mechanisms of evolution somehow Institute of Applied Life Sciences, Claremont, living orders of African placental mammals
contradict darwinian evolution. Shapiro, who California 91711, USA. form a monophyletic clade. Although Rose
often mentions the Afrotheria, he states: “No
morphological evidence supporting Afrothe-
ria has been found.” However, the Cretaceous
Mammals on the move representatives of modern mammalian orders
are unknown, and the lack of an early fossil
record for most groups may be responsible
black-and-white photographs, there are eight for any morphological gaps between them.
The Beginning of the Age of Mammals
by Kenneth D. Rose full-page colour plates with photographs of the Among the groups assigned to Afrotheria,
Johns Hopkins University Press: 2006. best-preserved fossils and reconstructions. Rose, on the basis of morphology, accepts the
428 pp. $150 Although the bulk of the book is devoted to monophyly of Hyracoidea, Elephantoidea and
this mammalian explosion, Rose starts at the Sirenia. But, against the molecular evidence,
Zofia Kielan-Jaworowska beginning of the mammals’ tale. Two intro- he assigns Tenrecidae and Chrysochloridae
Just looking at The Beginning of the Age of ductory chapters are followed by four on the not to Afrosoricida but to Insectivora; Macro-
Mammals by Kenneth Rose, with its Henri origin of mammals and their early evolution scelidea to the relatives of the Anagalida; and
Rousseau-style jacket picture, catapults the in the Mesozoic. finally Tubulidentata (not described because
reader right into enchanted Early Eocene The author no doubt faced a problem when of a lack of fossils) to the archaic Ungulata.
life. The book is a scholarly treatment of an dividing the rest of the book into chapters. Each chapter contains a systematic table
important period in the evolution of mam- Details about the roots of many groups are using linnaean taxa and a hierarchy of system-
mals. Mammals originated some 225 million hazy, and the earliest representatives of most atic units following Malcolm McKenna and
years ago, and for about 160 million years they

FORSCHUNGINST. SENCKENBERG, FRANKFURT


were small nocturnal creatures living in the
shadow of the dinosaurs. Most of them would
have been size of a shrew or rat, with only a
few being as big as a fox. When the dinosaurs
died out at the end of the Cretaceous, 65 mil-
lion years ago, mammals changed lifestyle and
started to increase their size, with many enter-
ing niches abandoned by the extinct giants.
This was the age of mammals.
Kenneth Rose’s book The Beginning of the
Age of Mammals is devoted to this explosion
of mammals, particularly their evolution dur-
ing the first half of the Cenozoic period. Rose
highlights in particular the development of
placental mammals in the Palaeocene and
Eocene (between 65 million and 33 million
years ago).
One of the charms of this book is the abun-
dance of figures, with many attractive recon-
structions of Eocene mammals. Some of these
have been made possible by the unusual pres-
ervation of complete mammalian skeletons
from the Middle Eocene in Messel, Germany.
Rose had an opportunity to collaborate with
German colleagues when describing some of
these mammals. As well as line drawings and Fossil skeletons of Middle Eocene mammals such as Kopidodon have been found in Messel, Germany.

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