Nano comes to life

To make progress in biotechnology, the discipline of software engineering will be key. Right?

After all, life is the outcome of what is known as the genetic code. Our biological metabolism is the execution of that code in our cells, extra cellular structures, organs, various circulatory systems, and so on. Admittedly, that code lacks documentation, and has no comments to guide our understanding. Indeed, it has been described as worse than the worst of human-written “spaghetti” code. Such is the complexity. But in due course, we can expect the painstaking application of methods of reverse software engineering to induce biology to give up its deepest secrets. Right?

Not so fast. The message in the recent new book by Oxford University Professor Sonia Contera, Nano Comes to Life, is that if we want to make better progress with biology, we need to increase our understanding of physics. Yes, physics – including mechanics, surface tension, electrostatic forces, dynamic motion, and so on.

Consider our DNA. Parts of our chromosomes consist of genes that cause our cells to create various proteins. The mapping of elements of chromosomes to specific proteins is, indeed, governed by a genetic code. The elucidation of that code has been one of the great triumphs of scientific endeavour in the last hundred years. That same endeavour, however, threw up a puzzle: large parts of our DNA – perhaps the majority of it – seem to be “junk”. It consists of multiple copies of genes that no longer create proteins. Various ideas developed for why these DNA segments exist – viewing them as self-serving, or “selfish”: they exist because they are copied into new generations, and that’s all there is to say about the matter.

However, there’s more than one level to think about our DNA. Yes, it consists of genes. But it also exists as a complex 3D structure, which folds and coils. Depending on the precise folding and coiling – and on whether some molecular groups known as methyls or acetyls are added into a kind of skin for the DNA – different genes are exposed to chemical interactions. We say that different genes can be turned “on” or “off”. Without the long chains of intermediary so-called “junk” DNA between various genes, these 3D interactions wouldn’t take place. The folding and coiling would be different. In other words, junk DNA may be purposeful after all, not in terms of its biochemical interactions, but in terms of its mechanical interactions.

One suggestion in Nano Comes to Life is that mechanical pressure on a cell can result in pressure on the nucleus of the cell, which can, in turn, change the precise 3D shapes of various chromosomes, altering which genes are turned on or off. In other words, external stresses and strains from the environment could directly alter the genetic expressions inside cells.

The limits of reductionism

The suggestion just given is but one example of a thesis which Nano Comes to Life brilliantly highlights: we should avoid becoming carried away with the methodology of reductionism. Reductionism looks for the causes of complex phenomena in a fuller analysis of the constituent parts of the larger system. To understand human biology we need to understand cells. To understand cells we need to understand chemistry. To understand chemistry we need to understand physics. To understand physics we need to understand mathematics. All that is true… but it is not the whole story.

I confess that when I hear people criticising reductionism, I become apprehensive. I half expect the conversation to continue as follows: we cannot understand biology in terms of chemistry, so that proves that aliens did it. Or that psychic telepathy exists. Or that humans are designed by a supernatural deity. Or that magic dwells deep in the universe. Or some other (unjustified) leap of faith.

However, emphatically, that’s not the kind of criticism of reductionism that you’ll find in Nano Comes to Life. Instead, the message is a kind of restatement of the saying often attributed to Einstein:

Everything should be made as simple as possible, but not simpler.

In other words, true progress in biology is likely to come, not from single-minded pursuits of individual lines of thinking, but, instead, from the interplay of multiple levels of understanding. That interplay can give rise to emergence.

Progress in multiple fields

Nano Comes to Life contains an impressive survey of fast progress that is being made in multiple labs around the world (in research universities and in commercial settings) precisely by adopting this multi-level thinking. The book brings readers up to date with remarkable recent research breakthroughs in techniques such as:

• DNA nanotechnology (including DNA origami),
• novel protein synthesis via nanotechnology,
• nanomaterials and transmaterials – which combine features of biological materials with those from outside biology,
• the creation of replacement organs, as well as “organs on a chip” (very useful for drug testing purposes),
• targeted cancer drug delivery systems,
• avoidance of the threat of growing antibiotic resistance,
• enhancing the immune system,
• and other aspects of what is known as nanomedicine.

The book also provides fascinating insight into the history and practice of cutting-edge laboratory science.

The context: a vision delayed

I’ve been aware of the field of nanotechnology since some time around the year 1990, when I came across the very first book written on that subject. That book was Engines of Creation: The Coming Era of Nanotechnology, by Eric Drexler (first published in 1986). Reading that book that significantly raised my awareness of the scale of the profound positive transformation that technology could in due course enable in the human condition. Reflecting the importance of that book on the subsequent trajectory of my thinking, a picture of me holding my copy of it was my cover photo on Facebook for a number of years.

(Thanks to Yanna Buryak for snapping this picture of me at just the right moment.)

Eric Drexler’s 1986 book foresaw the eventual deliberate systematic manipulation of matter to create myriad nanoscale levers, shafts, conveyor belts, gears, pulleys, motors, and more. In ways broadly similar to the marvellous operation of ribosomes within biological cells, specially designed nanofactories will be able to utilise atomically precise engineering to construct numerous kinds of new material products, molecule by molecule. But whereas the natural nanotechnology of ribosomes involves processes that evolved by blind evolution, synthetic nanotechnology will involve processes intelligently designed by human scientists. These scientists will take inspiration from biological templates, but can look forward to reaching results far transcending those of nature.

But despite the upbeat vision of Engines of Creation, progress with many of the ideas Drexler envisioned has proven disappointingly slow. Although the word “nanotechnology” has entered general parlance, it has mainly referred to developments that fall considerably short of the full vision of nanofactories. Thus we have nanomaterials, including nanowires and nanoshells. We have techniques of 3D printing that operate at the nanoscale. We have nanoparticles with increasing numbers of uses. However, the full potential of nanotechnology, envisioned all these years ago by Drexler, remains a future vision.

What Sonia Contera’s book Nano Comes To Life provides, however, is a comprehensive summary of progress within the last few years – and grounds for foreseeing continuing progress ahead.

Why the 2010s are the new 1830s

A clear sign of progress – at last – with nanomachines was the award of the Nobel Prize for Chemistry in 2016. This prize was jointly received by Fraser Stoddart from Scotland, Bernard Feringa from the Netherlands, and Jean-Pierre Sauvage from France, in recognition of their pioneering work in this field – such as finding ways to convert chemical energy into purposeful mechanical motion.

As the Nobel committee remarked, nanomachines in the 2010s are at a roughly similar situation to electrical motors of the 1830s: the basic principles of the manufacture and operation of these machines are just becoming clear. The scientists in the 1830s who demonstrated a variety spinning cranks and wheels, powered by electricity, could hardly have foreseen the subsequent wide incorporation of improved motors in consumer goods such as food processors, air conditioning fans, and washing machines. Likewise, as nanomachines gain more utility, they can be expected to revolutionise manufacturing, healthcare, and the treatment of waste.

It is these future revolutions which feature in Nano Comes to Life – particularly in the field of medicine and health. Importantly, these future revolutions are described in the book, not as any kind of inevitable development, but as something whose form and value will depend critically on choices taken by humans – individually and collectively. Indeed, in an epilogue to the book, the author points to a number of encouraging trends in how scientists, technologists, general citizens, and artists, are interacting to raise the probability that the full benefits of nanotechnology will be spread widely and fairly throughout society. It’s another example of the need to think about matters at more than one level at the same time.

The messages in that final section are ones with which I wholeheartedly agree.

Postscript: For a deeper dive

To hear Sonia Contera present her ideas in more depth, and to join a public Q&A discussion about the implications, check out the London Futurists event happening this Saturday (7th December).