Category Archives: Nanosocieties

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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Introducing Nanosocieties

Nanotechnology is a growing field of research that holds great promises in a wide range of areas. At the same time, it is also a very young area of research, and researchers of different background can quite liberally brand their research as “nano”. Nanotechnology also has the potential to challenge the way we perceive technology, and at the same time offer new ways of understanding biology. It is important that these issues are tackled not only from a perspective purely rooted in natural sciences, but from other disciplines as well. The idea behind this blog is to initiate a cross-disciplinary discussion on hos development in nanotechnology can be understood and what implications it has for the way we perceive technology

The field of nanotechnology is steadily expanding with an ever-growing number of publications associated with the keyword ”nanotechnology”. A search for the term in Thomson Reuters Web of Knowledge yields 15,696 hits (years 1945 to 2011). However, 9,815 of theses approximately 16,000 are published within the last five years. Funding of research in nanotechnology has also increased over the last few years and recently China overtook USA when it comes to funding research in nanotechnology. Both within and outside of the research community, the potential health risks associated with nanotechnology, especially concerning exposure to nanoparticles and fibers made from carbon nanotubes, are heavily debated. However, there is no consensus regarding exactly how the use of nanomaterials should be regulated in legislation and health issues associated with, for example, nano-scale particles has been a concern even before the growth of nano-science.

Since it seems that the question what should actually be defined as nanotechnology is still debated, it might be useful to approach the subject from another perspective. Let us instead consider length scales in technology in general and see what makes the nanometer scale different. In conventional technology, the properties of an object are not directly related to the properties of the molecules it is built from. A chair, for instance, is primarily an object crafted from a bulk material. Molecular properties are of course important, but they do no define the chair. In nanotechnology, which deals with technological devices with at least one dimension in the size range between one and one hundred nanometer, the properties of individual molecules are of far greater importance. It is also an area where different types of materials meet. George M. Whitesides writes in his 1991 paper “Molecular Self-Assembly and Nanochemistry: A Chemical Strategy for the Synthesis of Nanostructures” (Science, 1991):

Structures in this range of sizes can be considered as exceptionally large, unexceptional, or exceptionally small, depending on one’s viewpoint, synthetic and analytical technologies, and interests (Fig. 1) . To solid-state physicists, material scientists, and electrical engineers, nanostructures are small. The techniques, such as microlithography and deposition from the vapor, that are used in these fields to fabricate microstructures and devices require increasingly substantial effort as they are extended to the range below 102 nm. To biologists, nanostructures are familiar objects. A range of biological structures – from proteins through viruses to cellular organelles – have dimensions of 1 to 102 nm. To chemists, nanostructures are large. Considered as molecules, nanostructures require the assembly of groups of atoms numbering from 103 to 109 and having molecular weights of 104 to 1010 daltons.

Thus, there is an overlap between biological structures on a subcellular level, molecules created by organic synthesis and conventional solid technology constructed using lithography. This means that nanotechnological objects can be constructed using both biological and non-biological material. It can be created on a molecular scale or crafted from bulk materials.

Here, we se one of the interesting aspects of nanotechnology. As the size regime is in the interface between many different types of structures, there is a possibility to expand the types of materials used to create technology to include, for example, biological macromolecules or supramolecular assemblies. An important feature, which is common between nanotechnological and biological objects, is the foundation in self-assembly as a construction principle. This design principle, where the information determining the assembled structure is an emergent property arising from the interaction between the individual building blocks, enables the creation of devices on a scale not accessible by e.g. lithography.

So far, we have seen that biological and nanotechnological objects can be constructed in the same way, using self-assembly. However, the similarities do not stop there, many nanotechnological devices are constructed either to mimic biological functions, or constructed using biological molecules. Examples of the latter involve molecular scaffolds or molecular electronics built from DNA, or nano-scale containers composed of phospholipids, the molecules that make up the cell membranes shielding the interior of biological cells from the exterior environment. Because we have entered the length scale where biological molecules are relevant, it is now possible to consider new materials, which have not been seen as technological before, as such.

At the same time as nanotechnology incorporates more and more of biological functionalities and features there is and opposing trend in the other end of the spectrum: Biological cells are stripped of many of their most fundamental features to more and more resemble purely technological objects. The development of synthetic genomes, a field of research whose most well known representative is the scientist and entrepreneur Craig Venter, challenges the perception of the biological cell as something other than technological devices which can be designed and assembled using man made components.

When the boundaries between technology and biology, between culture and nature, diminish, it is important to also examine the mechanism that is perhaps most closely associated with biological life: Darwinian evolution. Evolution is essentially the process of repetition with error. Stripped down to these basic concepts, evolution is by no means restricted to the realm of biology. There are already examples where evolutionary processes are implemented as fundamental mechanisms in technology. Emphasis on evolutionary mechanisms is perhaps most prominently seen in computer programming in the creation of self-improving code, but also there are instances where this perspective is combined with the manufacturing of physical objects. The process that is perceived as biological evolution comprises a multitude of material relationships in them selves featuring both repetition and error. An in-depth understanding of these processes helps loosening the strong association between evolution and life that is so prevalent. With the growth of technology relying on self-assembly, the ubiquity of the evolutionary process becomes more and more apparent.

Now, what is the purpose of this discussion? We want to raise a discussion on what technology can be. When the borders molecular assemblies and processes from biology are used to create technology and, simultaneously, technology is used to, in a way, manufacture biological cells, it is important to ask the question: What is the effective difference between living and non-living objects? Does there have to be a distinction? The understanding of biological processes on a molecular level, e.g. the replication of DNA, the translation of genes into proteins or the control of cellular processes through chemical signaling, has had a fundamental effect on the way we think about life and all that it means. Nowadays, symbols like the double helix of DNA are ubiquitous, and phrases such as “it’s in our genes” are commonly found in advertising. Does nanotechnology, comprising molecular technology based on self-assembly principles, have the same potential to change what we understand as both technology and biology?

So far there are a lot of open question, we want to investigate if theories from disciplines other than the sciences can provide valuable insight into these questions. We also want to create a cross-disciplinary platform where people active in, or just interested in, nanotechnology, systems biology, science theory, sociology or computer science can meet and share ideas on the implications of novel technologies.