Synthetic biology – the debate heats up

Will it be possible to radically remodel living organisms so that they make products that we want? This is the ambition of one variant of synthetic biology; the idea is to take a simple bacteria, remove all unnecessary functions, and then patch the genetic code for the functions we want. It’s clear that this project is likely to lead to serious ethical issues, and the debate about these issues is beginning in earnest today. At a conference being held in Berkeley today, synthetic biology 2.0, the synthetic biology research community is having discussions on biosecurity & risk, public understanding & perception, ownership, sharing & innovation, and community organization, with the aim of developing a framework for the self-regulation of the field. Meanwhile, a coalition of environmental NGOs, including Greenpeace, Genewatch, Friends of the Earth and ETC, has issued a press release calling on the scientists to abandon this attempt at self-regulation.

Some of the issues to be discussed by the scientists can be seen on this wiki. One very prominent issue is the possibility that malevolent groups could create pathogenic organisms using synthetic DNA, and there is a lot of emphasis on what safeguards can be put in place by the companies that supply synthetic DNA with a specified sequence. This is a very important problem – the idea that it is now possible to create from scratch pathogens like the virus behind the 1918 Spanish flu pandemic frightens many people, me included. But it’s not going to be the only issue to arise, and I think it is very legitimate to wonder whether community self-regulation is sufficient to police such a potentially powerful technology. The fact that much of the work is going on in commercial organisations is a cause for concern. One of the main players in this game is Synthetic Genomics, inc, which was set up by Craig Venter, who already has some form in the matter of not being bound by the consensus of the scientific community.

In terms of the rhetoric surrounding the field, I’d also suggest that the tone adopted in articles like this one, in this weeks New Scientist, Redesigning life: Meet the biohackers (preview, subscription required for full article), is unhelpful and unwise, to say the least.

Nanoscale ball bearings or grit in the works?

It’s all too tempting to imagine that our macroscopic intuitions can be transferred to the nanoscale world, but these analogies can be dangerous and misleading. For an example, take the case of the buckyball bearings. It seems obvious that the almost perfectly spherical C60 molecule, Buckminster fullerene, would be an ideal ball bearing on the nanoscale. This intuition underlies, for example, the design of the “nanocar”, from James Tour’s group in Rice, that recently made headlines. But a recent experimental study of nanoscale friction by Jackie Krim, from North Caroline State University, shows that this intuition may be flawed.

The study, reported in last week’s Physical Review Letters (abstract here, subscription required for full article), directly measured the friction experienced by a thin layer sliding on a surface coated with a layer of buckminster fullerene molecules. Krim was able to directly compare the friction observed when the balls were allowed to rotate, with the situation when the balls were fixed. Surprisingly, the friction was higher for the rotating layers – here the ball-bearing analogy is seductive, but wrong.

In Seville

I’ve been in Seville for a day or so, swapping the Derbyshire drizzle for the Andalucian sun. I was one of the speakers in a meeting about Technology and Society, held in the beautiful surroundings of the Hospital de los Venerables. The meeting was organised by the Spanish writer and broadcaster Eduardo Punset, who also interviewed me for the science program he presents on Spanish TV.

As well as my talk and the TV interview, I also took part in a panel discussion with Alun Anderson, the former editor-in-chief of New Scientist. This took the form of a conversation between him and me, with an audience listening in. I hope they enjoyed it; I certainly did. As one would imagine, Anderson is formidably well- informed about huge swathes of modern science, and very well-connected with the most prominent scientists and writers. Among the topics we discussed were the future of energy generation and transmission, prospects for space elevators and electronic newspapers, Craig Venter’s minimal genome project, and whether we believed the premise of Ray Kurzweil’s most recent book, ‘The Singularity is Near’. Alun announced he would soon be appearing on a platform with a Ray Kurzweil’s live hologram, or thereabouts. However he did stress that this was simply because the corporeal Kurzweil couldn’t get to the venue in person, not because he has prematurely uploaded.

Computing, cellular automata and self-assembly

There’s a clear connection between the phenomenon of self-assembly, by which objects at the nanoscale arrange themselves into complex shapes by virtue of programmed patterns of stickiness, and information. The precisely determined three dimensional shape of a protein is entirely specified by the one-dimensional sequence of amino acids along the chain, and the information that specifies this sequence (and thus the shape of the protein) is stored as a sequence of bases on a piece of DNA. If one is talking about information, it’s natural to think of computing, so its natural to ask whether there is any general relationship between computing processes, thought of at their most abstract, and self-assembly.

The person who has, perhaps, done the most to establish this connection is Erik Winfree, at Caltech. Winfree’s colleague, Paul Rothemund, made headlines earlier this year by making a nanoscale smiley face, but I suspect that less well publicised work the pair of them did a couple of years ago will prove just as significant in the long run. In this work, they executed a physical realisation of a cellular automaton whose elements were tiles of DNA with particular patches of programmed stickiness. The work was reported in PLoS Biology here; see also this commentary by Chengde Mao. A simple one-dimensional cellular automaton consists of a row of cells, each of which can take one of two values. The automaton evolves in discrete steps, with a rule that determines the value of a cell on the next step by reference to the values of the adjacent cells on the previous step (for an introduction, to elementary cellular automata, see here). One interesting thing about cellular automata is that very simple rules can generate complex and interesting patterns. Many of these can be seen in Stephen Wolfram’s book, A New Kind of Science, (available on line here. It’s worth noting that some of the grander claims in this book are controversial, as is the respective allocation of credit between Wolfram and the rest of the world, but it remains an excellent overview of the richness of the subject).

I can see at least two aspects of this work that are significant. The first point follows from the fact that a cellular automaton represents a type of computer. It can be shown that some types of cellular automaton are, in fact, equivalent to universal Turing machines, able in principle to carry out any possible computation. Of course, this feature may well be entirely useless in practise. A more recent paper by this group (abstract here, subscription required for full paper), succeeds in using DNA tiles to carry out some elementary calculations, but highlights the difficulties caused by the significant error rate in the elementary operations. Secondly, this offers, in principle, a very effective way of designing and executing very complicated and rich structures that combine design with, in some cases, aperiodicity. In the physical realisation here, the starting conditions are specified by the sequence of a “seed” strand of DNA, while the rule is embodied in the design of the sticky patches on the tiles, itself specified by the sequence of the DNA from which they are made. Simple modifications of the seed strand sequence and the rule implicit in the tile design could result in a wide and rich design space of resulting “algorithmic crystals”.

a physical realisation of a cellular automaton executed using self-assembling DNA tiles

A physical realisation of a cellular automaton executed using self-assembling DNA tiles. Red crosses indicate propagation errors, which intiatiate or terminate the characteristic Sierpinski triangle patterns. From Rothemund et al, PLOS Biology 2 2041 (2004), copyright the authors, reproduced under a CREATIVE COMMONS ATTRIBUTION LICENSE

Lost comments

I apologise that a number of legitimate comments in recent days have been stopped by my spam filters – I’ve just rescued 6 of these from the moderation queue, where I had previously overlooked them amidst 519 spam comments. If you do make a comment which doesn’t appear (and this is most likely to happen to relatively long messages with lots of external links) you might want to alert me to this with a shorter comment. Anyway, my apologies to Brian Wang, Reza Fathollahzadeh, Moderate Transhumanist, NanoEnthusiast, sa. jafari and Michael Anissimov.

Nanoparticle toxicity: The Royal Society bites back

Last week saw a little bit more bad publicity for the nascent nano industry, in the shape of a news report from the BBC highlighting a call from the Royal Society for industry to disclose the data from its safety testing of free nanoparticles in consumer products. The origin of the report was a press release from the Royal Society, quoting Ann Dowling, the chair of the Royal Society/Royal Academy of Engineering study of nanotechnology.

The pretext for the Royal Society press release was the recent publication of an inventory of consumer products using nanotechnology by the Woodrow Wilson Centre Project on Emerging Nanotechnologies. But this call for disclosure was already one of the recommendations in the Royal Society’s report, and it’s not hard to sense the growing frustration within the Royal Society that, two years on from the publication of that report, we’re not much further forward in implementing many of its recommendations.

Transhumanism and radical nanotechnology

It’s obvious that there’s a close connection between the transhumanist movement and the idea of radical nanotechnology. Transhumanism is a creed which believes that human nature can and should be transcended with the aid of technological change, effectively leading to salvation both for individuals and society. Together with an expectation of the forthcoming singularity, a trust in cryonics (preservation of corpses at very low temperatures to await future revival) and an enthusiasm for radical life extension, the Drexlerian view of nanotechnology forms part of a belief package held by many transhumanists. The two main organisations devoted to promoting the radical view of nanotechnology, the Center for Responsible Nanotechnology and the Foresight Institute, are explicitly listed in a directory of transhumanist organisations from Michael Anissimov, of the Singularity Institute, who has also written a helpful overview of the transhumanist movement in his blog here.

Is this connection any cause for concern? Transhumanism as a movement has a fairly low profile generally, though blogger John Bruce has recently been exploring the movement and some of its supporters from a critical perspective (this link via TNTlog). But a very negative view of this relationship is presented by Joachim Schummer, a German philosopher now working at the University of South Carolina’s centre for nanoScience & Technology Studies: in an article “”Societal and Ethical Implications of Nanotechnology”: Meanings, Interest Groups, and Social Dynamics in the journal TechnĂ©.

Schummer, at the outset, insists on the quasi-religious character of transhumanism, characterising its creed as a belief in “futuristic technological change of human nature for the achievement of certain goals, such as freedom from suffering and from bodily and material constraints, immortality, and “super-intelligence.” He summarises its dependence on the Drexler vision of nanotechnology as follows:

“First, they foresee the development of Drexler’s “assemblers” that should manufacture abundant materials and products of any kind to be made available for everybody, so that material needs will disappear. Second, they expect “assemblers” to become programmable tool-making machines that build robots at the nanoscale for various other transhumanist aspirations—a vision that has essentially fuelled the idea of “singularity”. Thus, they thirdly hope for nanorobots that can be injected into the human body to cure diseases and to stop (or reverse) aging, thereby achieving disease-free longevity or even immortality. Fourth on their nanotechnology wish list are nano-robots that can step by step redesign the human body according to their ideas of “posthuman” perfection. Other nano-robots shall, fifth, make “atom-by-atom copies of the brain”, sixth, implement brain-computer-interfaces for “mind uploading”, seventh, build ultra-small and ultra-fast computers for “mindperfection” and “superintelligence”, and, eighth, revive today’s cryonics patients to let them participate in the bright future.”

Because of the central role to be played by nanotechnology in achieving personal and/or societal salvation, Schummer argues that transhumanists have an existential interest in nanotechnology; and are thus likely to much more accepting of the risks that nanotechnology might bring, on the grounds that the rewards are so great. He singles out the writing of Nick Bostrom, Chairman of the World Transhumanist Association, whose views he summarises thus: “In that mixture of radical utilitarianism and apocalyptic admonition, risks are perceived only for humanity as a whole, are either recoverable for humanity or existential for humanity, and only the existential ones really count. The risks of individuals, to their health and lives, are less important because their risks can be outweighed by steps towards transhumanist salvation of humanity.” Schummer comments that it is this “relative disregard for individual human dignity in risk assessments, i.e. the willingness to sacrifice individuals for the sake of global salvation, that makes transhumanism so inhumane.” Not that advanced nanotechnology is without risks; on the contrary, in the wrong hands it has the potential to destroy all intelligent life on earth. But since in the technologically deterministic view of transhumanists the development of nanotechnology is unavoidable, responsible people must rush to develop it first. Thus, “advancing nanotechnology is not only required for Salvation, but also a moral obligation to avoid Armageddon. “

It’s not surprising that transhumanists find it difficult to take an objective view of nanotechnology and the debates that surround it – to them, it is a matter whose importance, quite literally, transcends life and death.

On my nanotechnology bookshelf

Following my recent rather negative review of a recent book on nanotechnology, a commenter asked me for some more positive recommendations about books on nanotechnology that are worth reading. So here’s a list of nanotechnology books old and new with brief comments. The only criterion for inclusion on this list is that I have a copy of the book in question; I know that there are a few obvious gaps. I’ll list them in the order in which they were published:

Engines of Creation, by K. Eric Drexler (1986). The original book which launched the idea of nanotechnology into popular consciousness, and still very much worth reading. Given the controversy that Drexler has attracted in recent years, it’s easy to forget that he’s a great writer, with a very fertile imagination. What Drexler brought to the idea of nanotechnology, which then was dominated, on the one hand by precision mechanical engineering (this is the world that the word nanotechnology, coined by Taniguchi, originally came from), and on the other by the microelectronics industry, was an appreciation of the importance of cell biology as an exemplar of nanoscale machines and devices and of ultra-precise nanoscale chemical operations.

Nanosystems: Molecular Machinery, Manufacturing, and Computation , by K. Eric Drexler (1992). This is Drexler’s technical book, outlining his particular vision of nanotechnology – “the principles of mechanical engineering applied to chemistry” – in detail. Very much in the category of books that are often cited, but seldom read – I have, though, read it, in some detail. The proponents of the Drexler vision are in the habit of dismissing any objection with the words “it’s all been worked out in ‘Nanosystems'”. This is often not actually true; despite the deliberately dry and textbook-like tone, and the many quite complex calculations (which are largely based on science that was certainly sound at the time of writing, though there are a few heroic assumptions that need to be made), many of the central designs are left as outlines, with much detail left to be filled in. My ultimate conclusion is that this approach to nanotechnology will turn out to have been a blind alley, though in the process of thinking through the advantages and disadvantages of the mechanical approach we will have learned a lot about how radical nanotechnology will need to be done.

Molecular Devices and Machines : A Journey into the Nanoworld , by Vincenzo Balzani, Alberto Credi and Margherita Venturi (2003). The most recent addition to my bookshelf, I’ve not finished reading it yet, but it’s good so far. This is a technical (and expensive) book, giving an overview of the approach to radical nanotechnology through supramolecular chemistry. This is perhaps the part of academic nanoscience that is closest to the Drexler vision, in that the explicit goal is to make molecular scale machines and devices, though the methods and philosophy are rather different from the mechanical approach. A must, if you’re fascinated by cis-trans isomerisation in azobenzene and intermolecular motions in rotaxanes (and if you’re not, you probably should be).

Bionanotechnology : Lessons from Nature, by David Goodsell (2004). I’m a great admirer of the work of David Goodsell as a writer and illustrator of modern cell biology, and this is a really good overview of the biology that provides both inspiration and raw materials for nanobiotechnology.

Soft Machines : Nanotechnology and Life, by Richard Jones (2004). Obviously I can’t comment on this, apart from to say that three years on I wouldn’t have written it substantially differently.

Nanotechnology and Homeland Security: New Weapons for New Wars , by Daniel and Mark Ratner (2004). I still resent the money I spent on this cynically titled and empty book.

Nanoscale Science and Technology, eds Rob Kelsall, Ian Hamley and Mark Geoghegan (2005). A textbook at the advanced undergraduate/postgraduate level, giving a very broad overview of modern nanoscience. I’m not really an objective commentator, as I co-wrote two of the chapters (on bionanotechnology and macromolecules at interfaces), but I like the way this book combines the hard (semiconductor nanotechnology and nanomagnetism) and the soft (self-assembly and bionano).

Nanofuture: What’s Next For Nanotechnology , by J. Storrs Hall (2005). Best thought of as an update of Engines of Creation, this is a an attractive and well-written presentation of the Drexler vision of nanotechnology. I entirely disagree with the premise, of course.

Nano-Hype: The Truth Behind the Nanotechnology Buzz, by David Berube (2006). A book, not about the science, but about nanotechnology as a social and political phenomenon. I reviewed in detail here. I’ve been referring to it quite a lot recently, and am increasingly appreciating the dry humour hidden within its rather complete historical chronicle.

The Dance of Molecules : How Nanotechnology is Changing Our Lives , by Ted Sargent (2006). Reviewed by me here, it’s probably fairly clear that I didn’t like it much.

The Nanotech Pioneers : Where Are They Taking Us?, by Steve Edwards (2006). In contrast to the previous one, I did like this book, which I can recommend as a good, insightful and fairly nanohype-free introduction to the area. I’ve written a full review of this, which will appear in “Physics World” next month (and here also, copyright permitting).