Category Archives: Seeman

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.

DNA, genes and nanotechnologies – what they are and what they are not

One of the areas of research that exemplifies the interface between biology and nanotechnology and the raises new questions about what technology is and can be is the field of DNA nanotechnology. To address these questions, it is important to first understand what DNA is. In this post, we will move slowly through the world of DNA to analyze its function in biology, before finally arriving in the DNA nanotechnology.

Of all existing molecular structures, the double helix of DNA is probably one of the most well known. Schematic representations of DNA, showing a twisted, ladder-like structure are commonplace in advertising and popular culture. DNA plays an important role in the formation of societies on a multitude of levels, both living and non-living. The foundation to the importance of DNA lies in its ability to act as a carrier of information. In biological cells, DNA forms genes, which essentially are packages of information that can be translated into discrete objects that perform specific functions within the cell. DNA is transcribed into the bridging molecule RNA, which is, in turn, translated into a string of amino acids. Finally, the string of amino acids folds into a functional protein. DNA-RNA-protein – this is the central dogma of molecular cell biology. After being identified as the carrier of genetic information in 1944, and after the discovery of its double helical structure by James D. Watson in 1953 (Watson and Crick, 1953), DNA has been placed at the core of biology and, in a wider sense, bio-societies. By bio-societies I mean societies of living and non-living objects that are, in any way, transverse by biology. This includes societies of bio-molecules, cellular societies, and animal and human societies. (see previous post on Whitehead’s conception of societies)

In the context of bio-societies, genes have a very central position and interact in numerous ways. I would like to divide the function of genes in this context into two principal (albeit closely related) cases:

  1. The first case states that expression of a gene corresponds to a biological function and genetic differences can be associated to functional differences. Here, focus is the properties of the products from specific genes or groups of genes when expressed in an organism.
  2. The second case deals with genes as carriers of evolutionary information. The primary concern here is the evolutionary process and how it links organisms and properties together over space and time.

I want to do the division into two cases as they function in slightly different ways and need to be addressed somewhat differently. Here, we will mostly deal with the first case, how genes function. How genes act, and are acted upon, is in many was a matter of debate. One perspective places individual genes in the center of all biosocial interactions. This is perhaps most clearly expressed in Richard Dawkins’ The extended phenotype. Here, Dawkins states that

“Evolution is the external and visible manifestations of the differential survival of alternative replicators. Genes are replicators; organisms and groups of organisms …are vehicles in which replicators travel about” (Dawkins, 1982: 82).

In this gene-centric view, genes become very determining and dominating in the formation of bio-societies. The consequence of this is a world where genes become monolithic objects, free of all interrelations.

Donna Haraway labels this reductive position as gene fetishism. Gene fetishism mistakes genes as things-in-themselves and not as complex abstract assemblages.

“The gene as a fetish is a phantom object, lake and unlike the commodity. Gene fetishism involves “forgetting” that bodies are nodes in web of integrations, forgetting the tropic quality of all knowledge claims” (Haraway, 1997: 142).

Further,

“A gene is not a thing, much less a “master molecule” or a self-contained code. Instead, the term gene signifies a node of durable action where many actors, human and nonhuman, meet” (Haraway, 1997: 142).

Following a gene-centric perspective, there is a probability that genes become synonymous with DNA. When genes appear as discrete objects, it is tempting to only see the DNA sequence and not all the complex set of other factors acting upon DNA and influencing how the information coded in the DNA sequence is expressed. This way, we crate a misunderstanding of not only what genes are, but also what DNA is.

In order to describe DNA in a way that does not hide the society of object that form the assembled gene and where DNA does not automatically mean gene, we need to strip DNA of all its relations and focus on the molecule itself.

DNA is an abbreviation of deoxyribonucleic acid and is a polymer consisting of repeating nucleotide units. The backbone of the DNA polymer is built of the phosphate and sugar moieties of the nucleotides. In addition to this, the nucleotides also comprise a base moiety, which can be adenine (A), thymine (T), guanine (G) or cytosine (C). The bases form two separate pairs, A and T, and G and C. In the polymer, the nucleotide units form a sequence of bases that enables the assembly of the double helix together with another unpaired strand with a matching sequence of bases. It is this sequence of bases that is the code intrinsic to DNA and which gives DNA its information potential. However, DNA does not do anything on its own. What the information carried within the DNA sequence means is entirely dependent on the interrelation of DNA with other objects. In the gene fetishistic perspective this dependence on association is obscured.

Because the information stored in DNA depends of complex assemblies of a wide variety of objects, there is a potential to let DNA form other things than genes. This leads us to DNA nanotechnology. DNA nanotechnology is the non-biological utilization of the programmability of DNA to create nanometer scale DNA-based objects in a controlled way. In the 1980’s Nadrian Seaman pioneered the field of DNA nanotechnology creating molecular lattices made from DNA. (Seeman, 1982) The potential of DNA as a building block for technology is described by Seeman in an article in Nature in 2003:

“The nucleic acids seem to be unique …, providing a tractable, diverse and programmable system with remarkable control over intermolecular interactions, coupled with known structures for their complexes” (Seeman, 2003).

Instead of using the DNA code to construct genes, the base sequence of multiple strands is designed so that when they interact, a well-defined object is formed. Thus, the information contained within the DNA does no longer represent genes, but instead function as a manual for how the DNA molecules themselves should self-assemble into a specified shape.

A division can be made between two different types of DNA nanotechnology. Structural DNA nanotechnology deals with the creation of geometrical shapes and nano-scale machines. Here, the physical properties of the assembled structure are in focus. One of the most remarkable innovations in structural DNA-nanotechnology in recent years is DNA origami, which was invented in 2006 by Paul Rothemund. (Rothemund, 2006). DNA origami utilizes the genome from a virus together with a large number of shorter DNA strands to enable the creation of numerous DNA-based structures (Figure 1). The shorter DNA strands forces the long viral DNA to fold into a pattern that is defined by the interaction between the long and the short DNA strands.

DNA origami

Figure 1. Structures made from DNA using the DNA-origami method (Rothemund, 2006).

The second type instead uses the programmability of DNA to create devices that are capable of computing. Here, the structure of the assembled DNA is not of primary interest. Instead, control of the DNA sequence is used in the creation of computational algorithms, like e.g. artificial neural networks. (Qian et al., 2011)

In DNA nanotechnology, DNA is no longer treated as a distinctly biological object. Instead, DNA becomes a technological object with a potential to form new kinds of devices. This makes DNA a hybrid object, both biology and technology, both nature and culture. This way, DNA nanotechnology disrupts the unification of DNA and genes.

References

Dawkins, R. (1982). The Extended Phenotype: The Gene as a Unit of Selection. (London: Oxford University Press).

Haraway, D.J. (1997). Modest_Witness@Second_Millennium.Femaleman©_Meets_OncoMouse™ (New York: Routledge).

Qian, L.L., Winfree, E., and Bruck, J. (2011). Neural Network Computation with DNA Strand Displacement Cascades. Nature 475, 368-372.

Rothemund, P.W.K. (2006). Folding DNA to Create Nanoscale Shapes and Patterns. Nature 440, 297-302.

Seeman, N.C. (1982). Nucleic-Acid Junctions and Lattices. Journal of Theoretical Biology 99, 237-247.

Seeman, N.C. (2003). DNA in a Material World. Nature 421, 427-431.

Watson, J.D., and Crick, F.H.C. (1953). Molecular Structure of Nucleic Acids – a Structure for Deoxyribose Nucleic Acid. Nature 171, 737-738.

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