Monthly Archives: May 2012

A World of Machines

What constitutes a machine? Following a textbook definition, a machine is an assemblage of parts that transmit forces, motion or energy in a predetermined manner. Further, a machine not only works my transmitting energies, but also by transforming them. The first things that come to mind are perhaps complex industrial or proto-industrial contraptions designed to perform some kind of mechanical work.

machine

The driving force can be provided e.g. by electricity or chemical energy stored in hydrocarbons. Here we have both transformation of energy when the energy used to drive the machine is converted to motion as well as transmission when the motion is conveyed to the functional “output” of the machine. However, this concrete description is quite limiting and does not answer the question: What is the fundamental, abstract essence of machines? Levi Brynant elaborates on this in the post “Objects, Machines, and Engines”. Bryant states:

A machine is an entity that draws from something else and transforms it, full stop.

Further:

A spinning wheel is merely dormant, merely a dark object, without the foot of a man or woman to propel it. The foot provides a flow from which the spinning wheel draws in constituting its action. A spinning wheel is thus a machine attached to another machine. There is the spinning wheel as a machine and then the foot as a machine.

Thus, living organisms are also machines. By transformation of chemical energy, living organisms are able to sustain themselves and reproduce. Animals have since long been used as machines, e.g. pigs as transformators of waste products to edible biomass. Fieldclub writes in “Whey To Go: On The Hominid Appropriation of the Pig Function”:

The erosion of the forests heralded a significant intensification of the Pig Function, as pigs were absorbed into household economies and became ‘the Husbandman’s best Scavenger […]’. (Fieldclub, 2011: 128)

Further:

The Enclosures Acts, eliminating common land and limiting access to the remaining woods, produced a flow of deterritorialised labour power, […] leading to the mass exodus from the countryside and growth of the cities. In many cases, in a last attempt to hang on to the autonomy to which they were accustomed, they took with them their pigs, which continued to perform their function by eating the family’s waste. (Fieldclub, 2011: 128)

The machine-function of the living organism differs from that of the solid-state machine in the sense that (relatively) few of the transformations and transmissions in the living organisms rely on direct mechanical coupling. Take note that I do not use the word machine as a metaphor. Living organisms are not objects that resembles machines but machines in themselves in their transformation of energy.

If we take a closer look within the organism-machine at the level of the molecular and supramolecular assemblies that constitute it we find a multitude of systems that fit the previously mentioned textbook definition of machines.  Inside cells, motor proteins transport cargo along the cell skeleton by transforming energy stored in the chemical bonds of the nucleotide monomer adenosine triphosphate (ATP) to motion. The enzyme ATP synthase, responsible for producing ATP, the cell’s main energy currency, utilizes a rotary motion as a central part of its function . This motion cycles each of its three active sited between different activity states. Furthermore, motor proteins also create complex assemblages together with, amongst others, cell skeletal components to construct large-scale instruments for mechanical work such as bacterial flagella or muscles. Thus, in living organisms, machines exist on all scales, on the macromolecular, on the supramolecular on the organelle scale and as a whole organism.

In part inspired by diversity of molecular machines amongst living organisms, a range of molecular machines have been developed within the field of DNA nanotechnology.  In contrast to structural DNA-nanotechnology aimed at the constructions of rigid and well-defined assemblies, research on DNA-nanomachines tries to construct dynamic, DNA-based assemblies that behave in a predetermined way. DNA-machines use DNA, both to build the machine, but also as fuel. The energy gain associated with DNA-duplex formation can be used as a driving force for a DNA-based machine. A simple example of this is the DNA tweezers constructed by Yurke et al. (Yurke et al., 2000) The tweezers uses “fuel” and “anti-fuel” strands to cycle between open and closed forms, and in the process generates “waste” strands. Using similar principles, the DNA-machine concept has been expanded beyond the simple on-and-off functionalities of the DNA tweezers. Seeman and co-workers describe a biped DNA-walker with directional control. (Sherman and Seeman, 2004) The walker uses energy from sequential duplex formations and transforms it into directional motion across DNA footholds. In an introductory paragraph, the importance of control is illustrated with a reference to the Wright brothers:

The recent centennial of the Wright brothers’ invention of the airplane reminded the world not only of the fundamental importance of traveling machines but also that the great achievement of the Wright brothers was not so much getting off the ground, but controlling their biplane so it could fly steadily. One hundred years later, we find ourselves facing many of the same challenges on the nanometer scale. Numerous techniques have been devised for building or isolating molecular machines and motors, but the powerful combination of a wide range of motion with precise control has proved elusive. (Sherman and Seeman, 2004: 1203)

After the proof-of-principle examples, the DNA-walker concept has been developed in several ways. A recent example is the DNA spiders developed by Lund et al. (Lund et al., 2010). The three-legged spiders are able to walk along a pre-designed track on a DNA-origami rectangle. The energy driving the motion of the spider comes from the interaction with the underlying DNA support. When walking across the DNA landscape, the DNA robot enzymatically modifies the supporting DNA thus preventing backwards motion.

When walking, the spider reads a number of functions from the DNA-origami support, such as “follow”, “turn”, “start” or “stop”. This dependency on information from the environment is an important difference between molecular and conventional machines. Lund et al writes:

Traditional robots rely for their function on computing, to store internal representations of their goals and environment and to coordinate sensing and any actuation of components required in response. Moving robotics to the single-molecule level is possible in principle, but requires facing the limited ability of individual molecules to store complex information and programs. One strategy to overcome this problem is to use systems that can obtain complex behavior from the interaction of simple robots with their environment. (Lund et al., 2010: 206)

A related difference between biological and molecular machines compared to solid-state one has to do with connectivity. In conventional machines, constituting parts are directly connected through physical attachments, either in form of mechanical connections or through wires. In biology direct physical connections exist within e.g. individual proteins or defined supramolecular assemblies. However, there is no direct association between the chemical energy providing the driving force for the protein-machine and the actual machine function. Using Bryant’s terminology, the enzyme draws from the ATP-flow and the signal molecule flow. These flows simultaneously associate with multitudes of enzyme-machines. Contrastingly, the engineered macro-machine selects a limited number other machines, all (more or less) fixed to that one machine. On the larger scale of the organism-machine, connections are diffuse.  Signaling molecules have to move through three- and two-dimensional fluids in order to connect the various functionalities. On this scale, not only the transformation requires diffusive connectivity, but also the transmission. Where the solid-state machine consists of discrete parts, the organism-machine is rather represented by a fluid continuum. The molecular machines form some sort of middle ground with diffusive energy supply and signaling by with a well defined functional whole.

potatomachine

Tiempo, 2da. versión by Victor Grippo, as seen on the exhibition Animismus at Haus der Kulturen der Welt, Berlin.

As we have seen, machines can be very varied in both constitution and function. The image above shows a great number of different machines; the clock-machine draws upon the potato-machine. The potato-machine, in turn, draws upon the cell and molecular machines. What DNA-based nanotechnology does is that it makes it possible to select flows from molecular machines that are not accessible by conventional technology.

References:

Fieldclub (2011). Whey to Go: On the Hominid Appropriation of the Pig Function. Collapse 7, 119-147.

Lund, K., Manzo, A.J., Dabby, N., Michelotti, N., Johnson-Buck, A., Nangreave, J., Taylor, S., Pei, R., Stojanovic, M.N., Walter, N.G., et al. (2010). Molecular Robots Guided by Prescriptive Landscapes. Nature 465, 206-210.

Sherman, W.B., and Seeman, N.C. (2004). A Precisely Controlled DNA Biped Walking Device. Nano Letters 4, 1203-1207.

Yurke, B., Turberfield, A.J., Mills, A.P., Simmel, F.C., and Neumann, J.L. (2000). A DNA-Fuelled Molecular Machine Made of DNA. Nature 406, 605-608.