Genesis Machines: The New Science of Biocomputation by Martyn Amos
Bill Thompson investigates bio-computing with Martyn Amos
Something incredibly exciting is happening in molecular biology at the moment, as the combination of new techniques, improved experimental data and the latest conceptual framework unleashes a wave of creativity and scientific exploration.
The age of “synthetic biology” is upon us, a consequence of our greater understanding of how DNA makes RNA makes protein and deeper insight into the regulatory mechanisms that apply in the nucleus, the ways that cells are programmed to differentiate and operate, and the value of taking a computational approach to biological systems.
We are on the verge of creating molecular machines capable of turning genes on and off, synthesising novel molecules and exerting precise control over the inner functions of cells.
Already off-the-shelf “biobricks” allow researchers to build biologically-based systems to carry out defined tasks, and instead of uncovering the many mysteries of life through analytic techniques, taking cells and nuclei and genes apart in an attempt to understand how they work, we will soon be building our own systems from scratch, learning by doing.
And once we have built simple things like viruses we will move on to the big stuff, like tiny machines that will clear the prions from Alzheimer’s-ridden brains or target cancers.
This is a vitally important, fast-changing and little understood area, and it is unfortunate that Genesis Machines does such a bad job of explaining exactly what is going on or conveying the significance of recent breakthroughs.
Part of the problem is biographical. Amos is currently based at the Department of Computing and Mathematics at Manchester Metropolitan University, and holds what he describes as “the world’s first PhD in DNA Computing”, which he obtained back in 1997 when the potential of DNA as a basis for computation was only just being explored.
As a result he spends a significant proportion of the book talking about the ways in which DNA molecules can be used to carry out computational tasks that are normally done with transistors, silicon and logic gates, promising to explain where the next generation of computers are coming from, and why they are “nothing like we’ve seen before”.
Unfortunately it is now pretty clear that the exploration of biological molecules as a replacement for silicon-based computing is in fact a dead end. Yet Amos holds back from revealing this crucial information until two-thirds of the way through the book when, having gone into incredible detail about the way cleverly designed DNA sequences can solve shortest-path problems, he admits that trying to use DNA for solving mathematical problems is not going to happen, since “if the exponential curse doesn’t get you, the damage, the errors and the sheer cost will.” This extended detour into the cul de sac of DNA computing leaves too little space for a proper exploration of synthetic biology.
The style is also all over the place, with a poorly structured combination of journalistic profiles and basic science, weaving potted biographies and backgrounds of key figures like Len Adleman or Ron Mullis with populist explanations of genetics or the operation of DNA. Occasional lapses in continuity – I still have no idea who the “Alan” he refers to on page 183 might be – and far too many overblown claims, like the breathless pronouncement that “Ciliates are living Turing Machines!”, make reading even more of a burden, especially with a surfeit of unwarranted exclamation marks and portentous italics.
In the Epilogue Amos approaches the “very real and deep underlying concerns” that some of us may have about the techniques he has been covering in such an enthusiastic and excitable manner for the previous 300 pages. He even promises, in his last thousand words, to convince readers that “far from being potentially dangerous, this work has the potential to make the world a safer place” – complete with the emphasis on “safer”.
Sadly, just as he fails to convey the scientific details of synthetic biology in a way that would be intelligible to any reader who was not already familiar with the work, he also fails to address the very real concerns that it raises. I remain to be convinced that recreating the 1919 flu virus demonstrates scientific responsibility, or that asking DNA synthesis companies to “check orders against sequences from known harmful organisms” will do anything to deter tomorrow’s bioterrorists.
I wanted to enjoy this book, not least because understanding what is now possible in molecular biology is going to be increasingly important as we are presented with new therapies, new chemical manufacturing processes and perhaps even new forms of life.
But, in the end, reading Genesis Machines left me wishing that I had a clear, coherent and well-structured overview of just what is happening in the field of synthetic biology instead of this disappointing and ultimately uninformative text. ■
Genesis Machines is published by Atlantic Books